:: DESCRIPTION
CNT-MD is a software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael:
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
RECOMB 2017: 318-335
:: DESCRIPTION
The SBT (Sequence Bloom Tree) is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence
SSBT is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brad Solomon, Carl Kingsford (2016).
Fast search of thousands of short-read sequencing experiments.
Nature Biotechnology 34:300-302.
J Comput Biol. 2018 Jul;25(7):755-765. doi: 10.1089/cmb.2017.0265. Epub 2018 Mar 12.
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
Solomon B, Kingsford C
:: DESCRIPTION
SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.
:: DESCRIPTION
BayesTrees is a program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples.
::DEVELOPER
Reading Evolutionary Biology Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Serial NetEvolve is a modification of the Treevolve program in which serially sampled sequences are evolved along a randomly generated coalescent tree or network (Grassly et al. 1999; Hudson 1983; Kingman 1982) . Treevolve offers a variety of evolutionary model and population parameters including a rate of recombination and as such it was chosen over other programs to be adapted for the simulation of serially sampled data. The new features include the choice of either a clock-like model of evolution or a variable rate of evolution, simulation of serial samples and the output of the randomly generated tree or network in Newick format or in our newly formulated NeTwick format.
::DEVELOPER
Bioinformatics Research Group (BioRG)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2006 Sep 15;22(18):2313-4. Epub 2006 Jul 14.
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network.
Buendia P, Narasimhan G.
:: DESCRIPTION
PediTree is a software package to recursively analyse plant pedigree data which is arranged in a simple-single table database structure.
Peditree will lookup the parents of a variety/cultivar, then the parents of the parents (grandparents)and so on. The result is displayed in a explorer style, collapsible tree or a pedigree drawing (see images below; click to enlarge).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Hered. 2005 Jul-Aug;96(4):465-8. Epub 2005 Apr 13.
Peditree: pedigree database analysis and visualization for breeding and science.
van Berloo R, Hutten RC.
:: DESCRIPTION
phyutility (Phyloinformatic utility) is a Java program to perform simple but essential tasks on sequences and trees from the command line.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Smith, S. A. and Dunn, C. W. (2008)
Phyutility: a phyloinformatics tool for trees, alignments, and molecular data.
Bioinformatics. 24: 715-716
:: DESCRIPTION
Taxnameconvert is a commandline software that takes as input a file with a name table and usually a Newick formatted tree file or fasta sequence/alignment file, but can also be used to exchange names in many other text file formats.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GeoMeTree is a python program to compute the geodesic path between two phylogenetic trees.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J Comput Biol. 2008 Jul-Aug;15(6):577-91.
An exact algorithm for the geodesic distance between phylogenetic trees.
Kupczok A, Haeseler AV, Klaere S.