Table 1 Versions and additional options
From: Fast and robust multiple sequence alignment with phylogeny-aware gap placement
Versions and additional command-line parameters | ||
|---|---|---|
POA | poaV2 v1.0.0 | -do\_global -do\_progressive blosum80.mat |
Prank(+F) | v.111130 | +F -twice |
Prank | v.111130 | -twice |
ClustalW | 2.0.10 | |
MUSCLE(-i) | v3.8.31 | |
MAFFT(-i) | v6.843b | --retree 2 --maxiterate 1000 --globalpair |
MUSCLE | v3.8.31 | -maxiters 1 |
MAFFT | v6.843b | --retree 1 --maxiterate 0 |
ProGraphMSA | --mldist --cs_profile K4000.lib | |
(--estimate_aafreqs --end_indel_prob -1 --no_force_align_m) | ||
ProGraphMSA D | --mldist --darwin --cs_profile K4000.lib | |
(--estimate_aafreqs --end_indel_prob -1 --no_force_align_m) | ||