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T-REX (webserver)

Index T-REX (webserver)

T-REX() (Tree and Reticulogram Reconstruction) is a freely available webserver, developed at the department of Computer Science of the Université du Québec à Montréal, dedicated to the inference, validation and visualization of phylogenetic trees and phylogenetic networks. [1]

16 relations: Clustal, Distance matrix, FASTA format, Horizontal gene transfer, MAFFT, Multiple sequence alignment, MUSCLE (alignment software), Neighbor joining, Newick, Newick format, PHYLIP, Phylogenetic network, Phylogenetic tree, Robinson–Foulds metric, Université du Québec à Montréal, Web server.

Clustal

Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence alignment.

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Distance matrix

In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set.

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FASTA format

In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.

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Horizontal gene transfer

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring.

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MAFFT

In bioinformatics, MAFFT (for multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version of MAFFT used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the Fast Fourier Transform.

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Multiple sequence alignment

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.

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MUSCLE (alignment software)

MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences.

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Neighbor joining

In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987.

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Newick

Newick is a village, civil parish and electoral ward in the Lewes District of East Sussex, England.

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Newick format

In mathematics, Newick tree format (or Newick notation or New Hampshire tree format) is a way of representing graph-theoretical trees with edge lengths using parentheses and commas.

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PHYLIP

PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).

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Phylogenetic network

A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly)Huson, DH and Scornavacca, C (2011).

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Phylogenetic tree

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.

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Robinson–Foulds metric

The Robinson–Foulds metric is a way to measure the distance between unrooted phylogenetic trees.

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Université du Québec à Montréal

The Université du Québec à Montréal (UQAM) is a public university based in Montreal, Quebec, Canada.

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Web server

Web server refers to server software, or hardware dedicated to running said software, that can serve contents to the World Wide Web.

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Redirects here:

T-REX (Webserver).

References

[1] https://en.wikipedia.org/wiki/T-REX_(webserver)

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