:: DESCRIPTION
Ancestors is a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jan 1;26(1):130-1. doi: 10.1093/bioinformatics/btp600. Epub 2009 Oct 22.
Ancestors 1.0: a web server for ancestral sequence reconstruction.
Diallo AB1, Makarenkov V, Blanchette M.
:: DESCRIPTION
HaploShare was designed to find shared haplotypes among patients from a common recent ancestor.
::DEVELOPER
WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2015 May 9;16:92. doi: 10.1186/s13059-015-0662-9.
HaploShare: identification of extended haplotypes shared by cases and evaluation against controls.
Ying D, Sham PC, Smith DK, Zhang L, Lau YL, Yang W.
:: DESCRIPTION
Ortheus is a probabilistic method for the inference of ancestor (aka tree) alignments.It is primarily aimed at refining an initial (large-scale) genomic multiple-sequence alignment to create a multiple sequence ancestor alignment.
::DEVELOPER
Benedict Paten (benedict (AT) soe.ucsc.edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2008 Nov;18(11):1814-28. doi: 10.1101/gr.076554.108. Epub 2008 Oct 10.
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
:: DESCRIPTION
Ancestor is a software which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhang J, Nei M (1997)
Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods.
J Mol Evol 44(Suppl 1):S139-S146
:: DESCRIPTION
MGRA is a software for reconstruction of phylogenetic trees as well as ancestral genomes and applied it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the new notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. In particular, we applied \MGRA to analyze the primate–rodent–carnivore controversy in mammalian phylogeny, i.e., the alternative between the primate–rodent and primate–carnivore clades. MGRA provided the rearrangement-based evidence, albeit limited, for the primate–carnivore clade as opposed to the currently favored primate–rodent clade.
::DEVELOPER
Max Alekseyev and Pavel A. Pevzner
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Max Alekseyev, Pavel Pevzner
“Breakpoint Graphs and Ancestral Genome Reconstructions.”
Genome Res. 2009 May;19(5):943-57. Epub 2009 Feb 13.
