Multalign - align_sequences runs too long on real data
I've started 4 transcriptomes with multalign pipeline, and it is running >4 days on 5 cores for 1600 genes. What will be in the case of 30 species?
I think it is because MacSE aligner written in java. Muscle does this alignements in about ~2h using 1 core.
How can I speed up the computation? Can I use muscle manually in-between of stages instead of MacSE? Or MacSE also finds ORFs? Can I speed up MacSE? Maybe I could use Muscle for alignement and MacSE only for ORF finding?