Elisabeth Tillier, Andy Pang, Andrew Smith, Robert Charlebois, Paulo Nuin
Simprot1.04
// This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version.
// This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details.
Please cite:
Nuin PAS., Wang Z., and ERM Tillier. (2006) The accuracy of several multiple sequence alignments for proteins. BMC Bioinformatics 7:471.
Pang, A., Smith, A. Nuin, PAS and ERM Tillier. (2005) SIMPROT: Using an empirically determined Indel distribution in simulations of protein evolution. BMC Bioinformatics: 6:236.
Usage: simprot1.04_mac [OPTION...] -a, --alignment= name of output alignment file, in fasta format (default: null) -b, --branch= branch length scale multiplier (default: 1) -c, --eFactor= Evolutionary Scale factor for the distribution of indel lengths (default: 3) -d, --debug debug mode -f, --tree= name of tree file, only bifurcations are allowed (default: null) -g, --indelFrequency= the indel frequency for evolutionary time c (default: 0.03) -l, --maxIndel= the maximum insertion/deletion length (default: 2048) -p, --subModel= substitution model: 0 for PAM, 1 for JTT, 2 for PMB (default: 2) -r, --rootLength= root sequence length (default: 50) -s, --sequence= name of output sequence file (default: null) -j, --phylip= name of output phylip file (default: null) -x, --alpha= gamma alpha. Set to -1 for equal evolutionary rates (default: 1) -i, --interleaved= interleaved output (default: 0) -y, --benner= benner (default: 0) -v, --variableGamma= variable gamma (default: 0) -k, --bennerk= benner k factor (default: -2) -w, --indelWeight= indel weighting parameter (default: 0) -t, --extraTerminalIndels= extra terminal indels parameter (default: 0) -z, --rootSequence= name of root sequence file (default: null) -u, --indel distribution= name of indel distribution file (default: null) -o, --indel output= file to output length of indels as created (default: null) -h, --correlation file= Correlated site pairs: i j correlation, only one site per. Indels are disabled for this option. (default: null) -e, --variableBranch= variable branch length scale multiplier (default: 0) -m, --branchExtinction= branch extinction probability (default: 0) -q, --InsDelRatio= prob of insertion (1 - prob of deletion) (would be 0.5 for equal frequencies) (default: 0.5)
Help options: -?, --help Show this help message --usage Display brief usage message