diff --git a/R/get_big_pi.R b/R/get_big_pi.R
index 63ef571..d35dbdc 100644
--- a/R/get_big_pi.R
+++ b/R/get_big_pi.R
@@ -3,7 +3,7 @@
 #' big-PI Plant Predictor is a web server utilizing a scoring algorithm for prediction of GPI modification sites in plants.
 #'
 #' @aliases get_big_pi get_big_pi.default get_big_pi.character get_big_pi.data.frame get_big_pi.list get_big_pi.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence An appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id An appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param simplify A boolean indicating the type of returned object, defaults to TRUE.
diff --git a/R/get_espritz.R b/R/get_espritz.R
index d1b46ae..0e65843 100644
--- a/R/get_espritz.R
+++ b/R/get_espritz.R
@@ -3,7 +3,7 @@
 #' Espritz web server predicts disordered regions from primary sequence. It utilizes Bi-directional Recursive Neural Networks and can process proteins on a genomic scale with little effort and state-of-the-art accuracy.
 #'
 #' @aliases get_espritz get_espritz.default get_espritz.character get_espritz.data.frame get_espritz.list get_espritz.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param model One of c('X-Ray', 'Disprot', 'NMR'), default is 'X-Ray'. Determines the model to be used for prediction. See details.
diff --git a/R/get_hmm.R b/R/get_hmm.R
index d1c4bff..70ec66c 100644
--- a/R/get_hmm.R
+++ b/R/get_hmm.R
@@ -4,7 +4,7 @@
 #' of a protein sequence vs a profile-HMM database (Pfam-A).
 #'
 #' @aliases get_hmm get_hmm.default get_hmm.character get_hmm.data.frame get_hmm.list get_hmm.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param verbose Boolean, whether to print out the output for each sequence, defaults to FALSE.
diff --git a/R/get_netGPI.R b/R/get_netGPI.R
index 5a558fc..30bba4d 100644
--- a/R/get_netGPI.R
+++ b/R/get_netGPI.R
@@ -3,7 +3,7 @@
 #' NetGPI server offers GPI Anchor predictions
 #'
 #' @aliases get_netGPI get_netGPI.default get_netGPI.character get_netGPI.data.frame get_netGPI.list get_netGPI.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param splitter An integer indicating the number of sequences to be in each .fasta file that is to be sent to the server. Defaults to 2500. Change only in case of a server side error. Accepted values are in range of 1 to 5000.
diff --git a/R/get_phobius.R b/R/get_phobius.R
index e4f10a8..3ddf712 100644
--- a/R/get_phobius.R
+++ b/R/get_phobius.R
@@ -3,7 +3,7 @@
 #' Phobius web server is a combined transmembrane topology and signal peptide (N-sp) predictor. Currently only "normal prediction" of signal peptides is supported by the function.
 #'
 #' @aliases get_phobius get_phobius.default get_phobius.character get_phobius.data.frame get_phobius.list get_phobius.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param progress Boolean, whether to show the progress bar, at default set to FALSE.
diff --git a/R/get_pred_gpi.R b/R/get_pred_gpi.R
index 9e0d30b..a4d4b95 100644
--- a/R/get_pred_gpi.R
+++ b/R/get_pred_gpi.R
@@ -3,7 +3,7 @@
 #' PredGPI web server is a predictor of GPI modification sites.
 #'
 #' @aliases get_pred_gpi get_pred_gpi.default get_pred_gpi.character get_pred_gpi.data.frame get_pred_gpi.list get_pred_gpi.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences.Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param spec Numeric in the 0-1 range, indicating the threshold specificity.
diff --git a/R/get_signalp.R b/R/get_signalp.R
index 9a09e98..75f23dc 100644
--- a/R/get_signalp.R
+++ b/R/get_signalp.R
@@ -3,7 +3,7 @@
 #' SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
 #'
 #' @aliases get_signalp get_signalp.default get_signalp.character get_signalp.data.frame get_signalp.list get_signalp.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param org_type One of c("euk", "gram-", "gram+"), defaults to "euk". Which model should be used for prediction.
diff --git a/R/get_signalp5.R b/R/get_signalp5.R
index 5391734..8ff423f 100644
--- a/R/get_signalp5.R
+++ b/R/get_signalp5.R
@@ -3,7 +3,7 @@
 #' The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya.
 #'
 #' @aliases get_signalp5 get_signalp5.default get_signalp5.character get_signalp5.data.frame get_signalp5.list get_signalp5.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param org_type One of "euk", "gram-", "gram+" or "archea". Default is "euk". Are the protein sequences from Eukarya, Gram-negative Bacteria, Gram-positive Bacteria or Archaea.
diff --git a/R/get_targetp.R b/R/get_targetp.R
index 5e856a2..c34abb1 100644
--- a/R/get_targetp.R
+++ b/R/get_targetp.R
@@ -3,7 +3,7 @@
 #' TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). TargetP uses ChloroP and SignalP to predict cleavage sites for cTP and SP, respectively. For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.
 #'
 #' @aliases get_targetp get_targetp.default get_targetp.character get_targetp.data.frame get_targetp.list get_targetp.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param org_type One of c("non_plant", "plant"), defaults to "plant". Which models should be used for prediction.
diff --git a/R/get_tmhmm.R b/R/get_tmhmm.R
index ce897ff..4a068c3 100644
--- a/R/get_tmhmm.R
+++ b/R/get_tmhmm.R
@@ -3,7 +3,7 @@
 #' TMHMM server offers prediction of transmembrane helices in proteins
 #'
 #' @aliases get_tmhmm get_tmhmm.default get_tmhmm.character get_tmhmm.data.frame get_tmhmm.list
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param splitter An integer indicating the number of sequences to be in each .fasta file that is to be sent to the server. Default is 2500. Change only in case of a server side error. Accepted values are in range of 1 to 10000.
diff --git a/R/maab.R b/R/maab.R
index 25a2ecc..e629b81 100644
--- a/R/maab.R
+++ b/R/maab.R
@@ -3,7 +3,7 @@
 #' Perform Motif and amino acid bias classification of hydroxyproline rich glycoproteins according to Johnson et al. (2017)
 #' 
 #' @aliases maab maab.default maab.character maab.data.frame maab.list maab.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param order Order of motif counting, the default is as in Johnson et al. (2017).
diff --git a/R/predict_hyp.R b/R/predict_hyp.R
index cd733d1..acfc484 100644
--- a/R/predict_hyp.R
+++ b/R/predict_hyp.R
@@ -4,7 +4,7 @@
 #' It was trained on plant sequences with experimentally determined 4-hydroxyprolines from swissprot data base. Prediction is not possible for prolines which are within 10 N-terminal and 6 C-terminal amino acids (V1 model version) and 10 N-terminal and 7 C-terminal amino acids (V2 model version), they will be excluded from output.
 #' 
 #' @aliases predict_hyp predict_hyp.default predict_hyp.character predict_hyp.data.frame predict_hyp.list predict_hyp.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank. Ids should be unique.
 #' @param tprob A numeric value indicating the threshold for prediction. Acceptable values are in 0 - 1 range. At default set to 0.3 for "V1" model and 0.224 for "V2" model, offering a tradeoff between sensitivity and specificity.
diff --git a/R/scan_ag.R b/R/scan_ag.R
index 9ae9fb9..2afe091 100644
--- a/R/scan_ag.R
+++ b/R/scan_ag.R
@@ -4,7 +4,7 @@
 #' Where: O - hydroxyproline, A - alanine, S - serine, T - threonine, G - glycine and V - valine. This function attempts to find the mentioned dipeptides according to user specified rules. Since the positions of hydroxyprolines are usually unknown, all prolines are considered instead. If any sequence from the supplied contains "O" the function will consider only true AG glycomodules.
 #'
 #' @aliases scan_ag scan_ag.default scan_ag.character scan_ag.data.frame scan_ag.list scan_ag.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param dim An integer defining the minimum number of close dipeptides to be considered, at default set to 3.
diff --git a/R/scan_nglc.R b/R/scan_nglc.R
index 3629768..d9d6910 100644
--- a/R/scan_nglc.R
+++ b/R/scan_nglc.R
@@ -3,7 +3,7 @@
 #' Detection is based on PROSITE pattern PS00001. Mean local hydrophilicity (Hopp and Woods, 1981) is used to assess if the asparagines are buried.
 #' 
 #' @aliases scan_nglc scan_nglc.default scan_nglc.character scan_nglc.data.frame scan_nglc.list scan_nglc.AAStringSet
-#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param data A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param sequence A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param id A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
 #' @param span An integer specifying how many amino acids around the target asparagine residues is used to calculate hydrophilicity. At default set to 5: asparagine position - 5 to asparagine position +5 residues. Range to consider: 3 - 10. Acceptable values are 0 - 20.
diff --git a/man/get_big_pi.Rd b/man/get_big_pi.Rd
index 5bb3c7a..a2f2e77 100644
--- a/man/get_big_pi.Rd
+++ b/man/get_big_pi.Rd
@@ -33,7 +33,7 @@ get_big_pi(data, ...)
 \method{get_big_pi}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_espritz.Rd b/man/get_espritz.Rd
index 02a8837..995c363 100644
--- a/man/get_espritz.Rd
+++ b/man/get_espritz.Rd
@@ -34,7 +34,7 @@ get_espritz(data, ...)
 \method{get_espritz}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_hmm.Rd b/man/get_hmm.Rd
index d734dbc..ec8dd26 100644
--- a/man/get_hmm.Rd
+++ b/man/get_hmm.Rd
@@ -37,7 +37,7 @@ get_hmm(data, ...)
 \method{get_hmm}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_netGPI.Rd b/man/get_netGPI.Rd
index a3612ff..8dcb161 100644
--- a/man/get_netGPI.Rd
+++ b/man/get_netGPI.Rd
@@ -25,7 +25,7 @@ get_netGPI(data, ...)
 \method{get_netGPI}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_phobius.Rd b/man/get_phobius.Rd
index 2865652..d50ed51 100644
--- a/man/get_phobius.Rd
+++ b/man/get_phobius.Rd
@@ -25,7 +25,7 @@ get_phobius(data, ...)
 \method{get_phobius}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_pred_gpi.Rd b/man/get_pred_gpi.Rd
index ae7cf41..058be14 100644
--- a/man/get_pred_gpi.Rd
+++ b/man/get_pred_gpi.Rd
@@ -25,7 +25,7 @@ get_pred_gpi(data, ...)
 \method{get_pred_gpi}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences.Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_signalp.Rd b/man/get_signalp.Rd
index 05253d7..bed8dd5 100644
--- a/man/get_signalp.Rd
+++ b/man/get_signalp.Rd
@@ -39,7 +39,7 @@ get_signalp(data, ...)
 \method{get_signalp}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_signalp5.Rd b/man/get_signalp5.Rd
index e7330d6..ea8fc49 100644
--- a/man/get_signalp5.Rd
+++ b/man/get_signalp5.Rd
@@ -32,7 +32,7 @@ get_signalp5(data, ...)
 \method{get_signalp5}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_targetp.Rd b/man/get_targetp.Rd
index 70ce423..9abfd55 100644
--- a/man/get_targetp.Rd
+++ b/man/get_targetp.Rd
@@ -38,7 +38,7 @@ get_targetp(data, ...)
 \method{get_targetp}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/get_tmhmm.Rd b/man/get_tmhmm.Rd
index 3565b98..cea5a87 100644
--- a/man/get_tmhmm.Rd
+++ b/man/get_tmhmm.Rd
@@ -25,7 +25,7 @@ get_tmhmm(data, ...)
 \method{get_tmhmm}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/maab.Rd b/man/maab.Rd
index 7d3aa0d..40d1c6f 100644
--- a/man/maab.Rd
+++ b/man/maab.Rd
@@ -32,7 +32,7 @@ maab(data, ...)
 \method{maab}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/predict_hyp.Rd b/man/predict_hyp.Rd
index b20f21f..b61830e 100644
--- a/man/predict_hyp.Rd
+++ b/man/predict_hyp.Rd
@@ -30,7 +30,7 @@ predict_hyp(data, ...)
 \method{predict_hyp}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/scan_ag.Rd b/man/scan_ag.Rd
index f59c91c..b0ce103 100644
--- a/man/scan_ag.Rd
+++ b/man/scan_ag.Rd
@@ -33,7 +33,7 @@ scan_ag(data, ...)
 \method{scan_ag}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}
 
diff --git a/man/scan_nglc.Rd b/man/scan_nglc.Rd
index f765f55..ad01d55 100644
--- a/man/scan_nglc.Rd
+++ b/man/scan_nglc.Rd
@@ -25,7 +25,7 @@ scan_nglc(data, ...)
 \method{scan_nglc}{AAStringSet}(data, ...)
 }
 \arguments{
-\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class "SeqFastaAA" resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.}
+\item{data}{A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.}
 
 \item{...}{currently no additional arguments are accepted apart the ones documented bellow.}