Output also the position of original alignments withing the concatenated alignment about catfasta2phyml HOT 2 CLOSED

Thank you Ales for your suggestion. And I know, it is indeed a good feature to have - and it have actually been on my todo list (for a long time). For some reason I can't remember, I did not include that feature immediately, but settled with some basic info that might help you construct such info on your own.

If you run the script with the option --verbose, the info on the size of individual input files is printed to standard error (see example below). You have to do the summation on your own for now I'm afraid.

$ catfasta2phyml.pl --verbose m*d.fas > apa

Checking sequences in infiles...

  File m1d.fas:  ntax=23 nchar=1303
  File m2d.fas:  ntax=23 nchar=1042
  File m3d.fas:  ntax=23 nchar=394

Checked 3 files -- sequence labels and lengths seems OK.
Concatenated 23 sequences, total length 2739.
Printing concatenation to STDOUT.


End of script.

from catfasta2phyml.

This table is now the output (STDERR) from the program (commit 6bad419).

Recommended usage:

catfasta2phyml.pl *.fas > combined.phy 2> combined_partitions.txt

from catfasta2phyml.