Tree estimation fails on short alignment

[wash]

For the the following alignment we can't calculate the background model and phyml gives this strange warning and asks for a user input "type any key to exit" which is super annoying.

 a score=0

 s mm9.chr2 94496640 4 + 0 GAAA

 s hg18.chr11 91392746 4 - 0 GAAA

 s panTro2.chr11 90665046 4 - 0 GAAA

 s rheMac2.chr14 28971164 4 + 0 GAAA

 s canFam2.chr18 29504980 4 + 0 GAAA

[JanLeipzig]

It is still highly annoying!!!

[svenderheld]

The issue is annoying but it is related to the phyml-package which RNAcode utilizes for tree estimation and not to RNAcode directly. It is not obvious when it appears:

a score=0
s mm9.chr2 94496640 4 + 0 TTTC
s hg18.chr11 91392746 4 - 0 TTTC
s panTro2.chr11 90665046 4 - 0 TTTC
s rheMac2.chr14 28971164 4 + 0 TTTC
s canFam2.chr18 29504980 4 + 0 TTTC
-> results in the same error

a score=0
s mm9.chr2 94496640 4 + 0 GTTT
s hg18.chr11 91392746 4 - 0 GTTT
s panTro2.chr11 90665046 4 - 0 GTTT
s rheMac2.chr14 28971164 4 + 0 GTTT
s canFam2.chr18 29504980 4 + 0 GTTT
-> terminates successfuly

Most of the other reported issues are related to phyml as well. We, therefore, try to replace the old version of phyml by the most recent one. Please note, that this needs some non-trivial refactoring of our own code, which we avoided so far.