:: DESCRIPTION
QuickTree allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
QuickTree: building huge Neighbour-Joining trees of protein sequences.
Howe K, Bateman A and Durbin R
Bioinformatics 2002;18;11;1546-7
:: DESCRIPTION
MPP (Microarray-to-Phylogeny-Pipeline) is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposonbased insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.
::DEVELOPER
DICKS COMPUTATIONAL BIOLOGY GROUP
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Davey RP, Savva G, Dicks J and Roberts IN (2007)
MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets.
Bioinformatics 23 (8): 1023-1025
:: DESCRIPTION
DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kuhner, M. K. and J. Felsenstein. 1994.
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
Molecular Biology and Evolution 11: 459-468 (Erratum 12: 525 1995).
:: DESCRIPTION
Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages. It will also draw lineages-through-time-plots.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
STC (shortest triplet clustering algorithm) is a software to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2) time for n sequences.
::DEVELOPER
Center of Integrative Bioinformatics Vienna (CIBIV)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Le Sy Vinh and Arndt von Haeseler,
Shortest Triplet Clustering: Reconstructing Large Phylogenies,
BMC-Bioinformatics.6:92. 2005.
:: DESCRIPTION
CoSpec (short for CoSpeciation) is a simple Macintosh Classic application that can be used to show the coevolutionary behaviours of two phylogenies, one dependent on the other.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
