Get independent of Gblocks

[iimog]

We use Gblocks to filter the alignments in this line: https://github.com/molbiodiv/bcgTree/blob/dceaf223a92679e399aab367ca3ef29f618d94b7/lib/bcgTree.pm#L227 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 ?