Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F24%3A00604984" target="_blank" >RIV/60077344:_____/24:00604984 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12310/24:43908800 RIV/00216208:11310/24:10485273

Výsledek na webu

<a href="https://doi.org/10.1002/cpz1.969" target="_blank" >https://doi.org/10.1002/cpz1.969</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/cpz1.969" target="_blank" >10.1002/cpz1.969</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher

Popis výsledku v původním jazyce

PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. (c) 2024 Wiley Periodicals LLC.Basic Protocol 1: Constructing a phylogenomic datasetBasic Protocol 2: Performing phylogenomic analysesSupport Protocol 1: Installing PhyloFisherSupport Protocol 2: Creating a custom phylogenomic database

Název v anglickém jazyce

Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher

Popis výsledku anglicky

PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. (c) 2024 Wiley Periodicals LLC.Basic Protocol 1: Constructing a phylogenomic datasetBasic Protocol 2: Performing phylogenomic analysesSupport Protocol 1: Installing PhyloFisherSupport Protocol 2: Creating a custom phylogenomic database

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/EF16_019%2F0000759" target="_blank" >EF16_019/0000759: Centrum výzkumu patogenity a virulence parazitů</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Current Protocols

ISSN

2691-1299

e-ISSN

2691-1299

Svazek periodika

4

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

19

Strana od-do

e969

Kód UT WoS článku

001253146600018

EID výsledku v databázi Scopus

2-s2.0-85182842858