Merging many (n=1600) fasta gene alignments into one core genome.

[musta1234]

Hello,

I have 1600 fasta aligned bacterial genes from mafft. Each aligned file contains about 442-446 strains.
I want to create a single multi-fasta alignment file for use in raxml. Is there a tool out there that will take these file and give me a merged alignment file?

Any ideas welcome.

gene1.aln
>strain_a
ATGC--ATG
>strain_b
GCG---ATG

gene2.aln
>strain_a
ATGC--ATG
>strain_b
GCG---ATG

[yzzhang]

Some tools like Gblocks can do this. However, it needs all the input alignment files contain same number of sequences and their order should be same. You said the aligned files contain different number of sequences (442~446), so you need to fix the alignment files first, then it is easy to get the merged fasta file using Gblocks.