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Table 1 Program version numbers and command-line options

From: Accelerated large-scale multiple sequence alignment

Version

Program

Options

1.83

ClustalW

-type = dna

2.04

Kalign

--nuc

6.811

MAFFT

--nuc

3.8.31a

MUDISC

-seqtype rna -maxiters 2

3.8.31a

MUSCLE

-seqtype rna -maxiters 2

2

POA

-do_global -do_progressive

  1. MUDISC and MUSCLE additionally use the option "-termgaps full" on BRAliBase and "-termgaps ext" on MDSA when assessing alignment quality. MUDISC, MUFPGA, and MUSCLE use the options "-termgaps full -seqtype dna -gapopen 0 -center -300 -maxiters 2" for the performance test.
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BMC Bioinformatics

ISSN: 1471-2105

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