Get independent of Gblocks

[iimog]

We use Gblocks to filter the alignments in this line:

bcgTree/lib/bcgTree.pm

Line 227 in dceaf22

$cmd = $self->{'gblocks-bin'}." $out/$gene.aln -t=p -b4=4 -b5=h";

So we are keeping blocks of length at least 4 with at least half the positions being non-gaps (see Gblocks documentation). This task can probably be performed by a simple script that we could include in the distribution. Gblocks is quite dated and a dependency that users need to get and install themselves. Therefore, getting rid of this requirement would be nice.

[jianshu93]

Hello @iimog,

Since you also mentioned this, trimAl is more updated and can be used for any modern CPUs (even M1/2/3 series by Apple). Check it here: https://github.com/inab/trimal

I think get rid of Gblocks is important because it is not supported by new CPUs like M series. Should be easy work (several lines of modification I presume).

Thanks,

Jianshu

[iimog]

Cool, thanks for the suggestion. I have not used trimal before, but it looks almost like a drop-in replacement. However, it still probably needs some testing, whether results are similar to those with Gblocks. What do you think @chiras ?