The input sequence file is an alignment of nucleotide or amino acid sequences. We accept three types of sequence files, which are fasta, nexus or phylip. The sequence data set must be in sequential format for nexus or phylip. It is recommended that the sequence name is comprised of alphabetical characters, digits or underscore. The program will replace any other characters with underscore "_".
Example for Nexus file in sequential format:
#NEXUS BEGIN DATA; DIMENSIONS NTAX=6 NCHAR=80; FORMAT DATATYPE=DNA MISSING=? GAP=- ; MATRIX [ 10 20 30 40 50 60 70 80 ] [ . . . . . . . . ] ES9v3ed_1 ATGAAAGTGAAGCCGAGCAGGAGGAATTATCAGCACTTGTGGTGGGGCATCATGCTCCTTGGGATGTTAATGATCTGTAA [80] ES9v1e2_1 ATGAAAGTGAAGCCCAGCAGGAGGAATTATCAGCACTTGTGGTGGGGCATCATGCTCCTTGGGATGTTAATGATCTGTAA [80] ES9v1e4_1 ATGAAAGTGAAGGGGAGCAGGAGGAATTATCAGCAGTTGTGGTGAAGCATCATGCTCCTTGGGATGTTAATGATCTGTAA [80] ES9v1e11_1 ATGAATGTGAAGGGGAGCAGGAGGAATTATCAGCAGTTGTGGTGAAGCATCATGCTCCTTGGGATGTTAATGATCTGTAA [80] ES9v1e3_1 ATGAAAGTGAAGCGGAGCAGGAGGAATTATCAGCACTTGTGGTGAAGCATCATGCTCCTTGGGATGTTTTTGATCTGTAA [80] ES9v1e6_1 ATGAATGTGAAGGGGAGCAGGAGGAATTATCAGCACTTGTGGTGAAGCATCATGCTCCTTGGGATGTTTTTGATCTGTAA [80] ; END;
Example for phylip file in sequential format:
6 80 ES9v3ed_1 ATGAAAGTGAAGCCGAGCAGGAGGAATTATCAGCACTTGTGGTGGGGCATCATGCTCCTTGGGATGTTAATGATCTGTAA ES9v1e2_1 ATGAAAGTGAAGCCCAGCAGGAGGAATTATCAGCACTTGTGGTGGGGCATCATGCTCCTTGGGATGTTAATGATCTGTAA ES9v1e4_1 ATGAAAGTGAAGGGGAGCAGGAGGAATTATCAGCAGTTGTGGTGAAGCATCATGCTCCTTGGGATGTTAATGATCTGTAA ES9v1e11_1 ATGAATGTGAAGGGGAGCAGGAGGAATTATCAGCAGTTGTGGTGAAGCATCATGCTCCTTGGGATGTTAATGATCTGTAA ES9v1e3_1 ATGAAAGTGAAGCGGAGCAGGAGGAATTATCAGCACTTGTGGTGAAGCATCATGCTCCTTGGGATGTTTTTGATCTGTAA ES9v1e6_1 ATGAATGTGAAGGGGAGCAGGAGGAATTATCAGCACTTGTGGTGAAGCATCATGCTCCTTGGGATGTTTTTGATCTGTAA
A text file contains a newick tree. Users can input their own tree to reconstruct COT tree and sequence based on the input tree. If branch lengths are associated with input tree, HyPhy will ignore them and estimate branch lengths.
Phylogenetic tree output (When user-specified tree is not provided)
A newick tree estimated by PhyML under GTR (DNA) or LG (amino acid) substitution model. The tree can be viewed through the ATV Java applet.
Evolutionary parameters output (When user-specified tree is not provided)
A set of evolutionary parameters estimated by PhyML.
A newick tree reconstructed by HyPhy. The tree can be viewed through the ATV Java applet.
COT sequence reconstructed by HyPhy under GTR (DNA) or LG (amino acid) substitution model.