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Simple Phylogeny specifications


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


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

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

[…] ttp:// (Masoudi-Nejad et al. ). Contigs and singletons were aligned with Clustal Omega ( The alignment file was submitted to Simple Phylogeny ( to produce a phylogenetic tree revealing the degree of relatedness among different sequences. […]


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

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 […]


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

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 and Simple Phylogeny (available at for protein multiple alignments and phylogenetic tree construction, respectively (the alignment and phylogenetic t […]


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

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 ( and visualized with ClustalW2 Simple Phylogeny ( […]


Programmatic access to bioinformatics tools from EMBL EBI update: 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 […]


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

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 (; ). […]

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