Accept '.' as gap character

[bernt-matthias]

'.' is frequently used as gap character.

Should be easy to add:

https://github.com/wash/rnacode/blob/fe20868df016f3be20351bcbdcecd89cb4d65003/phyml/utilities.c#L4484

and here

https://github.com/wash/rnacode/blob/fe20868df016f3be20351bcbdcecd89cb4d65003/phyml/utilities.c#L4521

Error output is currently also not very helpful:

Unknown character state : �

[bgruening]

We could patch the conda package, if this project is dead?

[bernt-matthias]

Either this - or fork it base the conda package on the fork. Then also others could contribute.