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prefix.seqs |
List of sequence files to use. The first sequence is taken as the reference sequence, refseq.fasta or refseq.gbk. |
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seqname.fasta seqname.gbk |
FASTA and/or GENBANK-format sequence files. |
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seqname.fasta.orfs seqname.gbk.orfs |
CDS annotation. Use the corresponding sequence coordinates, not alignment coordinates; the first nt is 1 not 0. (CDS files are only needed for the reference sequence if refpos = 1. CDS files are extracted from seqname.gbk file headers, where available, if gbkpos = 1.) |
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refseq.fasta.features or refseq.gbk.features |
Optional list of annotated features to include on plots. Use reference sequence coordinates. |
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prefix.pairs |
Optional list of sequence pairs to use. Otherwise the sequence pairs are taken from the phylogenetic tree. |