RecPars - Parsimony analysis of DNA sequences

The program recpars performs a parsimony analysis of a set of DNA sequences. It tries to find the best phylogenies for different segments of the sequences and thereby postulating a recombination event between these segments. A more thoroughly explanation can be found in

A Heuristic Method to Reconstruct the History of Sequences subject to Recombination. Jotun Hein. In Journal of Molecular Evolution, 36: 396--406, 1993.

Download

The implementation of recpars is done in C. To install recpars, download recpars.tar.gz, unpack it (tar xzf recpars.tar.gz), and run make in the subdirectory rec created during unpacking. The use of recpars is described in the README file distributed together with the source code.

WWW interface

Substitution costs:
	A	C	G	T	-
A
C
G
T
-
Options:
Recombination cost:
Initial phylogeny:
Rounds:
One phylogeny:
Debug:
Aligned sequences (phylip sequential format):
5 1000 Sequence1 tttgggactgagggcgaagactagtgctttacttgtctagccgtatttctgttccctgttgcgagatacccgtacattttgtgaatcgtacgcggctgcaaacgctctgattaatatcactgacgtacactcggcgtcaacaccgttctaccgtgtcgtagtcgcatcttatccaatcgcatataccgcaatacttagtgtggtgaaaggcccatatcttgtatgaggtggtagatgtggcgttcggaacagcaatgagtcaactactggagtgattgtaagtccgacatatatccttgatttatacggcgtgccaatccacgggtggctaatccctgaaacgcagcgagcatagtttttactctcgccagtagcgcccggcttggagcggactctgtagggggtaattccagcagagccgaagctcttgcggtgtcgcgtcgtccctatttctccgacccagtttgtagagcgctgctgaccgtgttattgcgtcccatgtacacattatcataatcctccgggccggcaaatcggcgtcaccatgtctagtcaaagtggcccatttttattgaacgggtgcctctacgcgatatttagttacccttcgcgaatataagttaccatagtggtcatactttagcggagatggtggggagtggcgatcaacataccatacgttcttgcacaatgtcaacgtgattgcaggctgttgggatcggcataacaaaagtccgtacgcacgatttccgcaggaccggaattgtagcaatgaggtaccattcgccgctcggggcgcgcgctctttccaggattgatagtgccacgttgcgctgcgtcaagaactttcgtagacgttgttcagttaaaaggccttggcgggggggttgtatggtggcgttatgacacgcagaatggctctttcaaacttgtggaatggagatagaatcagctcgattttactttggctctcgcgtttagatttgggctccccatgacc Sequence2 gacgggactgacggcgaagactagtgctttacgtgtctaggcgtatttctggtccctgttgcgagatccccgtacattttgtaaatcatacgcggctgcaaacgctctgattaatatcactgacggacactgggcgtcaacaccgctctaccgtgtcgtcgtcgcatcttatccaatcgcatacaccgcaactcttagtgtggtgataggcccatatcatgtatgagatggtagatggggcgttcgcaacggcaatgagtcaactagtggagggactgtaagtctgacatatatccatgatttacacggcgtgcccatccacggggggctaatccctgaaacacagcgagactgttttttactcccgcaagtagagaccggcatggagcggactctgtagggggaaattccagcagagccgaagctcatgcggtgtcgcgtcgtccctgattctccgagccgatttggagggcactgctgaccgggttattccgtcccatgtacacattatcatagtcctccgggccggcaaatcggcatcgccatgtctagtcccagtgtctcatttttattgaaggggtgcctctacgcgatattcagttacccttcgcgaatatgagttaccatactggtcatactttagcggagatgctggggagtgtcgatcaacatgccttacgttcatccacaatgtagacgtgattgcaggctgttgggatcggaatagcaaaagccggtacgcacgatttccgcaggacctgacttgtagcaatgcgttaccatacgccgctcggggcgcgtgctctttccaggatggttattgccacgttgcgctgcgtcaagaactgtcggtctggtttttcagttaaaagaccttggcgggggggttgcatggtggcgttatgacacgcataatggctcgttcaaacttgttgattggagatagaatcagctcgatattacttaggctctgtcgtttagatttgggctcgccatgacg Sequence3 gtcgggactgacggcgaagactagtgctttacgggtctagccgtatttctgttccctgttgcgagatacccgtacattttgtgaatcgtacgcggctgcaaacgctctgattaatatcactgacgtacactcggcgtcaacaccgttataccgtgtcgtagtcgcatcttatccaatcgcatataccgcaattcttagtgtggtgaaaggcccatatcttgtatgaggtggtagatgtggcgttcggaacagcaatgagtcaactactggagtgattgtaagtctgacatatatccttgatttatacggcgtgccaatccacgggtggctaatccctgaaacgcagcgagcatagtttttactctcgccagtagcgcccggcatggagcggactctgtagggggtaattccagcagagccgaagctcttgcggtgtcgcgtcgtccctatttctccgacccagtttgtagagcgctgctgaccgtgttattgcgtcccatgtacacattatcataatcctccgggccggcaaatcggcgtcaccatgtctagtcaaagtggcccatttttattgaacgggtgcctctacgcgatatttagttacccttcgcgaatataagttaccatattggtcaaactttagcggagatgctggggagtggcgatcaacataccatacgttcttgcacaatgtcaacgtgattgcaggctgttgggatcggcataacaaaagtcggtacgcacgatttccgcaggaccggaattttagcaatgaggtaccatacgccgctcggggcgcgcgctctttccaggattgttagtgccacgttgcgctgcgtcaagaactttcgtacacgttgttggctatgcggtcgtgatagaaggagatctaaatgataagtcagataacgataatgccacacctcgagctagtgcgggcctataggcttagcttaatgaatgacttcttctcggctctgcgtaaggtctccccattacg Sequence4 gtcgggactgacggcgaagactagtgctttacgtgtctagccgtatttctgttccctgttgcgagatacccgtacattttgtgaatcgtactcggctgcaaacgctctgattaatatcactgacgtacactcggcgtcaacaccgttctaccgtgtcgtagtcgcatcttatccaatcgcatatacctcaattcttagggtggtgttacgcccttttcatgtactggtttgttggtgtggcatttgcaacggtaatcaggctactagtagggtggtcgttagtccgacaaatatacatgagttaaagcgtgacctcatccaacggtggctatttgatgagagaaagctggcctattctatactttgtagagccgcgagtggcatggagcggacccactagtaggtttgtacagctgatgcgaatctcatgcggtgttgcgcccaccctttgtctccgacacagataggaggttactgccgacggagctattgggtccctacgacacggtacggtagtcatccgccgcttttcatcttccttaccacgtaaattcagcgggtttcgtctcgaatgagccggagcctcttcccggcatttatttaccatgcgcgactagtggttaccatcgtgtccatcctgtaaccgagatgcttgggcgaggggaacaacctgccaaacgcacacacaccatcagagcgaggaggcatgcccatgatatggacttatagataggcggtagggagcatttccccaagacgggaatcgtagcagtgtggtacctgccacagcacagggagttcactcgttccaggaattttagcgcctcgatccgctggttcgagcgctgtggtactgggcgttggctatgctgttgtggtaggaggagatctaaatgatcagtcttctaacgatagtgcctcacctcgacttgttgatcggagatagaatcagctcgattttactttggctctggcgtttagatttgggctacccatgacg Sequence5 ttcggaattgacggcgaagactactgctttagttgtgcacccgtattactgtccccgcgtgcgagatacacgtggattttttggatcgtcggcgtattcaaacgctccgtcgaatattaccgacgtacattcggcgcaaacagaaaacgaccttgtggtagtcgcatcttaagcactcgcatataccggaaatcgtggtatcgtattacgcccttttcatgtactggtttgttgctgtaacatttgcaacggtaatcgggctactagtagggtggtcgttcgtccgacaaatatacatgagtttaagcgtaacctcatccagcggtggctatttgatgagacaaagctggcctattctatactaggtagagccgcgagtggcatggagcggacccactagtagggttgtacagctgatgcgaatctcatgtggtgttgcgcccaccctttgtctccgacacagataggaggttacggccgacggagctattgggtccctaggacacggtacggtagtcatccgcagcttttcatcttccttaccacgtaaagtcagcgggtttcgtctagaacgagccggagcctcttcccggcatttatttaccatgggcgactagtggttaccatcgtgtccatcctgtaaccgagatgcttgggcgaggggaacatcctgccaaacgcacacacaccatctgagcgagaaggcatgcccatgatatggacttatagataggcggtagggagcatttccccaagacgggaatcgtagcagtgtgatacctgacacagctcagggagttcgggcgttccaggaattttagcgccccgatccgctggttcgagcgctttggtactgggcgttgtctatgctgttgtggtaggaggagatctaaatgatcagtcatcgaacgatagtgcctcacctcgacttgttgagcggagatagaatcagctcgattttactttggctctggcgtttagatttgggctacccatgacg