Computational phylogenetics
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about ...
Scientist says researchers in immigrant-friendly nations can't use his software
Gangolf Jobb, who developed Treefinder, has banned its use in eight European countries and the U.S.
7 reported dead, over 300 injured, after blast rocks busy Chinese port (VIDEOS, PHOTOS)
Two blasts shook the northeastern Chinese city of Tianjin late on Wednesday. State media has reported that over 300 people have been injured, and at least 7 are dead.
New Family Tree Illuminates 'Big Bang' in Bird Evolution After Dinosaur Extinction
A massive genetics project has produced the most comprehensive bird family tree ever, an embarrassment of scientific riches for studying everything from how birds evolved so quickly after dinosaurs di...
Why did Europeans suddenly disappear 4,000 years ago? Experts reveal evolutionary mystery - and say the makers of Stonehenge may hold the key | Mail Online
Researchers say the rapid expansion of the Bell Beaker culture, which is believed to have been instrumental in building the monoliths at Stonehedge, could hold the key to why the genetic lineage of Eu...
Substitution model
In biology, a substitution model describes the process from which a sequence of characters changes into another set of traits. For example, in cladistics, each position in the sequence might correspon...
Scientist says researchers in immigrant-friendly nations can't use his software
Gangolf Jobb, who developed Treefinder, has banned its use in eight European countries and the U.S.
7 reported dead, over 300 injured, after blast rocks busy Chinese port (VIDEOS, PHOTOS)
Two blasts shook the northeastern Chinese city of Tianjin late on Wednesday. State media has reported that over 300 people have been injured, and at least 7 are dead.
New Family Tree Illuminates 'Big Bang' in Bird Evolution After Dinosaur Extinction
A massive genetics project has produced the most comprehensive bird family tree ever, an embarrassment of scientific riches for studying everything from how birds evolved so quickly after dinosaurs di...
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohyd...
Conserved sequence - Wikipedia
Align-m
Align-m is a multiple sequence alignment program written by Ivo Van Walle.Align-m has the ability to accomplish the following tasks:
DIALIGN-T
DIALIGN-T is an implementation of an improved algorithm for segment-based multiple sequence alignment, written by Amarendran R. Subramanian and freely available under the GNU Lesser General Public Lic...
Distance matrices in phylogeny
Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to pr...
Bayesian inference in phylogeny
Bayesian Inference of Phylogeny uses a likelihood function to create a quantity called the posterior probability of trees using a model of evolution, based on some prior probabilities, producing the m...
BLAST
In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucl...
BLAST - Wikipedia
PANDIT (database)
PANDIT is a database of multiple sequence alignments and phylogenetic trees covering many common protein domains.
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutiona...
Sequence alignment - Wikipedia
List of phylogenetics software
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and b...
List of phylogenetics software - Wikipedia
Probalign
Probalign is a sequence alignment tool that calculates a maximum expected accuracy alignment using partition function posterior probabilities. Base pair probabilities are estimated using an estimate s...
Joseph Felsenstein
Joseph "Joe" Felsenstein (born May 9, 1942) is Professor in the Departments of Genome Sciences and Biology and Adjunct Professor in the Departments of Computer Science and Statistics at the University...
Joseph Felsenstein - Wikipedia
PHYLIP
PHYLIP (PHYLogeny Inference Package) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 35 portable programs, i.e. the source code...
Quartet distance
The quartet distance is a way of measuring the distance between two phylogenetic trees. It is defined as the number of subsets of four leaves that are not related by the same topology in both trees.<...
HYPHY (software)
HYPHY (/ˈhaɪfaɪ/ HY-fy) is a free multiplatform (Mac, Windows and UNIX) Computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipp...
Maximum parsimony (phylogenetics)
In biology, phylogenetics is the study of evolutionary relationships among groups of organisms, the vast majority of whose ancestral organisms are long extinct. It is therefore a matter of speculatio...
Maximum parsimony (phylogenetics) - Wikipedia
ProbCons
ProbCons is an open source probabilistic consistency-based multiple alignment of amino acid sequences. It is an efficient protein multiple sequence alignment program, which has demonstrated a statisti...
ProbCons - Wikipedia
MAFFT
MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. MAFFT is freely available for academic use, without any warranty.
DIALIGN-TX
DIALIGN-TX is a multiple sequence alignment program written by Amarendran R. Subramanian and is substantial improvement of DIALIGN-T by combining greedy and progressive alignment strategies in a new a...