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Protocols

Simple Phylogeny specifications

Information


Unique identifier OMICS_17615
Name Simple Phylogeny
Interface Web user interface
Restrictions to use None
Input data A multiple sequence alignment.
Input format Clustal, FASTA, MSF
Output format Clustal, Distance Matrix, NEXUS
Computer skills Basic
Stability Stable
Maintained Yes

Simple Phylogeny citations

 (6)
library_books

Structure, target specificity and expression of PN_LNC_N13, a long non coding RNA differentially expressed in apomictic and sexual Paspalum notatum

2017
Plant Mol Biol
PMCID: 5778186
PMID: 29119346
DOI: 10.1007/s11103-017-0679-4

[…] ttp://www.genome.jp/tools/egassembler/) (Masoudi-Nejad et al. ). Contigs and singletons were aligned with Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/). The alignment file was submitted to Simple Phylogeny (http://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/) to produce a phylogenetic tree revealing the degree of relatedness among different sequences. […]

call_split

More than Enzymes That Make or Break Cyclic Di GMP—Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli

2017
MBio
PMCID: 5635695
PMID: 29018125
DOI: 10.1128/mBio.01639-17
call_split See protocol

[…] Protein sequence alignments were performed with Clustal Omega and phylogenetic analyses with Simple phylogeny (both accessible at http://www.ebi.ac.uk/tools). […]

library_books

Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous

2017
BMC Genomics
PMCID: 5516332
PMID: 28724407
DOI: 10.1186/s12864-017-3942-9

[…] cis-regulatory element websites were visited for the last time on March 28, 2017).Phylogenetic analysis was carried out using Clustal Omega (available at http://www.ebi.ac.uk/Tools/msa/clustalo) and Simple Phylogeny (available at http://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny) for protein multiple alignments and phylogenetic tree construction, respectively (the alignment and phylogenetic t […]

library_books

The ATP dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities

2017
PMCID: 5512084
PMID: 28533432
DOI: 10.1074/jbc.M117.779470

[…] , CHD2 O14647, INO80 Q9ULG1, SNF2H O60264, hBRM P51531, and BRG1 P51532; others given earlier) were aligned with Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/) and visualized with ClustalW2 Simple Phylogeny (http://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/).3 […]

library_books

Programmatic access to bioinformatics tools from EMBL EBI update: 2017

2017
Nucleic Acids Res
PMCID: 5570243
PMID: 28431173
DOI: 10.1093/nar/gkx273

[…] New tools include: HMMER3 (), that uses probabilistic models called hidden Markov models for searching sequence databases for sequence homologs; Simple_Phylogeny, which replaces ClustalW2_Phylogeny and that provides access to phylogenetic tree generation methods; PredComp (), that compares a set of predicted annotations against actual automate […]

call_split

The Multidrug Resistance 1 Gene Abcb1 in Brain and Placenta: Comparative Analysis in Human and Guinea Pig

2014
PLoS One
PMCID: 4213008
PMID: 25353162
DOI: 10.1371/journal.pone.0111135
call_split See protocol

[…] rtional to the number of amino acid substitutions per site, of guinea pig, mouse, rat and hamster Abcb1 proteins and human ABCB1 was performed using phylogeny.fr (http://www.phylogeny.fr/version2_cgi/simple_phylogeny.cgi; ). […]


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