Flot (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments Molecular Ecology Ressources 10 (1): 162-166 link
Constant positions file (.const), if any:
If no .const file is inputted, the FASTA alignment will only contain variable positions.
PHASE output file (.out or .out_pairs):
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.
Sort sequences in alphabetical order
New! Reduce input (recommended for some downstream applications, such as phylogenetic analyses)
Examples: .out file, .out_pairs file, and .const file from the previous dataset
Frequently Asked Questions
Email the author
To return to Step 1, click here.