Flot (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments Molecular Ecology Ressources 10 (1): 162-166 [link]
|Genotypes to be phased|
Alignment of sequences from homozygous individuals and from heterozygotes to be phased (FASTA, one sequence of IUPAC one-letter codes per individual)
|Fake haplotype pairs|
Alignment of fake haplotype pairs from heterozygotes to be phased (FASTA, two sequences per individual). In this alignment, sequences for a given individual should have the same name except for the last character (for instance: "sample1a" for the first haplotype of sample 1, "sample1b" for the other).
Fake haplotype pairs are an alternate way of entering genotypes to be phased that is particularly useful when dealing with length-variant heterozygotes (since there is no IUPAC sign for "A or indel", "C or indel", etc.), but I rather recommend solving such cases first using Champuru then inputting the result as known haplotype pairs in the 3rd SeqPHASE input field (below).
|Known haplotype pairs|
Alignment of known haplotype pairs, if any (FASTA, two sequences per individual).
Since PHASE only accepts numbers and not letters for nucleotides at multistate characters, ? and N (missing information) have been replaced with ? or -1 (depending on whether the position displays two or more than two different nucleotides), - with 0, A with 1, C with 2, G with 3 and T with 4 in seqphase.inp (the main PHASE input file).
A known phase file has also been generated to tell PHASE which phases are already known and which ones are to infer.
In order to reduce PHASE running time, constant positions have been removed from the dataset. These constant positions have been stored in seqphase.const interspersed with periods (.) representing variable positions.
Once PHASE has been run, please proceed here to convert the PHASE output into a FASTA alignment (only the file seqphase.out is needed for this final step). (The above link will automatically pass the content of the .const file - if any - to the next step.)