You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
The text was updated successfully, but these errors were encountered:
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).
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 ?
We use
Gblocks
to filter the alignments in this line:bcgTree/lib/bcgTree.pm
Line 227 in dceaf22
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.The text was updated successfully, but these errors were encountered: