#36 Warning against using phylip2fasta.sh

[jnylander]

The script phylip2fasta.sh removes gap symbols (-) from the multiple sequence alignments. This is undocumented (as fas as I can tell. Nothing mentioned when issuing phylip2fasta.sh -h).

Input format for this script is a file in the "phylip format" which is a commonly used format for multiple sequence alignments (MSA), which is a file where all sequences have the same length. Length differences in such files are commonly accomodated by using "gap characters", very often the dash (-). It makes no sence removing those when converting a phylip MSA to a MSA in Fasta format.

Suggestion:

Change default format to NOT to remove gap symbols, or at least add this to the built-in documentation.