Hello all,

I am working on a phylogenetic analysis with 23 bacterial genomes.

I generated the gene clusters with panaroo and am now making gene trees for individual clusters.

The issue is that I am working with the single copy orthologues and have a directory full of .aln.fas multiple sequence alignments. The directory has thousands of alignments in it, and i only need the alignments with a gene sequence (header) for each taxa (n=23).

is there a one liner capable of grabbing all of the .aln.fas files with only 23 headers and piping them in to a list?

Therefore allowing me to easily put them into a new directory and generate the gene trees.

best,

AAH