nylander/catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

catfasta2phyml's Issues

Concatenated alignment in .xmfa format?

Hi,
I found your tool a few weeks ago and it has helped me a lot! However I was wondering, is it possible to get the output/concatenated alignment in .xmfa format? If not, do you know of some other tool for that?

Thanks in advance,
Julia

Excluding taxa not present in all files

Hi,
I was wondering if the tools have any option for exclude the taxa that's not present in all the files,

Thanks in advance,
Luis.

order of concatenated sequences

Hi,
I've used your tool in the past, it's very useful. The old version concatenated the fasta files exactly as they were listed on the command line. The new version however does not do that. Is that intended or a bug?
best wishes
Aldert

Output also the position of original alignments withing the concatenated alignment

Not an issue, rather a suggestion: it would be great if catfasta2phyml would be outputting also the positions of the individual alignments in the concatenated alignment.
E.g. if 1st alignment is 100 and 2nd alignment 200 characters long, the additional output file would continue following info:
Alignment1.fasta 1 100
Alignment2.fasta 101 300
...which could be used for e.g. defining the partitions for downstream phylogeny reconstruction using the concatenated alignment.
(I was using FASconCAT by Patrick Kueck can do this but seems to be much slower than your tool)
Best,
Ales

Warnings when concatenating

Recently when concatenating a data set I got:

    $ catfasta2phyml.pl --concatenate --fasta \
        ali_nov/*.fas > concat.faa 2> concat.partitions
    $ head -3 concat.partitions
    Use of uninitialized value in repeat (x) at /home/nylander/bin/catfasta2phyml.pl line 148.
    Use of uninitialized value in addition (+) at /home/nylander/bin/catfasta2phyml.pl line 197.
    ali_nov/TC000024.fas = 1-120

Still need to confirm and debug (Tue Nov 15).