Conserved regions of an alignment

Question

[l.souza]

Hello,

Is there any tool that I can find conserved regions of an alignment and create a list with them?

Answer 1

[h.mon]

Maybe trimAl can do what you need. Latest version download on GitHub.

[l.souza]

Correct me if I'm wrong, but trimAl removes the non-conserved regions and makes a new sequence with the conserved regions. I'd like to have a list with the conserved regions (and informations like their coordinates, window size, etc) inside the alignment.

[h.mon]

Maybe these options?

   -sgc        Print gap percentage count for columns in the input alignment.
   -scc        Print conservation values for columns in the input alignment.
   -sident     Print identity statistics for all sequences in the alignemnt. (see User Guide).

[l.souza]

These options doesn't show me neither the coordinates nor the window size!

[h.mon]

See some perl code here, you can modify it to match your needs.