Flot (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments Molecular Ecology Ressources 10 (1): 162-166 [link]
| PHASE output file (.out or .out_pairs) | ||
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If a .out file is inputted, a list of phased haplotypes will be returned as FASTA with 1-letter indetermination code letters (R, W, M, Y, S or K) at positions where phase certainty is inferior to a certain threshold (90% if PHASE default running options were used). If a .out_pairs file is inputted, a list of all possible haplotype pairs for each individual will be returned as FASTA with their respective probabilities shown between parentheses. |
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| Constant positions file (.const), if any | ||
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If no .const file is inputted, the FASTA alignment will only contain variable positions. |
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| Sort sequences | ||
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Sort sequences in alphabetical order. |
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| Reduce sequences | ||
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Reduce output (recommended for some downstream applications, such as phylogenetic analyses) |
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