Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?

Question

[Kumar]

I am trying to concatenate mafft and gblock processed multiple gene alignment files/sequences and make supermatrix by using FASconCAT-G v1.0, However, I end up with an error as follows,

!FILE-ERROR!: Unequal sequence lengths in file gene1.fasta!
READ IN gene1.fasta

Is there any way to fix this issue or could you suggest any other tool to do the same.

Thanks in advance.

[h.mon]

I would suggest you to check if all sequences have the same length at the file gene1.fasta, and fix their lengths if they differ.

[Kumar]

@h.mon, Yes, I have different length sequences in my gene1.fasta file. Can't I concatenated different length alignment file?. Moreover, I have more than 2000 alignment files, so manual curation is tedious to do. Therefore, could you please suggest any other tool, which can serve my purpose.

[h.mon]

How did you end up with different length sequences? MAFFT should add - to pad all alignments to the same length, and then Gblocks only remove columns, so all sequences should still have the same length. If the sequences do not have the same length, they may be improperly aligned, I would suggest you check the alignments for correctness (and review your analysis steps) before proceeding.

If you believe your alignments to be correct, you may try BeforePhylo, among several other tools. When I did this, I coded my "in house" - luckily for everyone, they are long gone.