FastME protocols

View FastME computational protocol

FastME statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Phylogenetic inference chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

FastME specifications

Information


Unique identifier OMICS_15882
Name FastME
Interface Web user interface
Restrictions to use None
Input data A data alignment file, a protein alignment file, and a distance matrix.
Input format PHYLIP
Output data The inferred phylogenies.
Programming languages C
Computer skills Basic
Version 2.0
Stability Stable
Registration required Yes
Maintained Yes

Documentation


Maintainer


  • person_outline Olivier Gascuel <>

Information


Unique identifier OMICS_15882
Name FastME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A data alignment file, a protein alignment file, and a distance matrix.
Output data The inferred phylogenies.
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL https://gite.lirmm.fr/atgc/FastME/
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Olivier Gascuel <>

Publications for FastME

FastME in pipelines

 (5)
2018
PMCID: 5698912
PMID: 29188023
DOI: 10.5256/f1000research.13945.r27739

[…] genes; see associated data repository . using these single-copy orthogroups, gene trees were first constructed, then the species tree was inferred using the distance-based method implemented by fastme . the resultant species tree (see associated data repository ) exhibits strong congruence to the phytophthora phylogeny recently published by , providing more evidence that the genome assembly […]

2018
PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334

[…] ngstools package to estimate all pairwise genetic distances. using the output file from the previous command, neighbor-joining trees were reconstructed with the genetic distances using the program fastme ver. 2.1.5 () with the command:, fastme–2.1.5–linux64 –d 1 –i $distance_file –o $tree, phylogenetic trees were diagramed using the web interface itol ver. 3.4.3 (http://itol.embl.de/) ()., […]

2017
PMCID: 5541404
PMID: 28768476
DOI: 10.1186/s12862-017-1020-1

[…] clustered., a rapid k-mer based approach (mash) was used to create reduced representations of selected bacillus genomes, and a fast distance-based phylogenetic analysis of this data (fastme) was performed to determine which species should be included in b. cereus s. l. the complete genomes of eight b. cereus s. l. species were annotated de novo with prokka, and these annotations […]

2012
PMCID: 3575317
PMID: 23114024
DOI: 10.1186/1471-2164-13-577

[…] with seqboot version 3.67 []. distance matrices were calculated for the initial alignment as well as for each of the 500 resamples using dnadist version 3.67 []. trees were then created using fastme from ncbi [] and the tree from the original alignment was compared to the 500 trees from the resamples using comparetobootstrap []., figtree (http://tree.bio.ed.ac.uk/software/figtree/) […]

2011
PMCID: 3158115
PMID: 21714939
DOI: 10.1186/1745-6150-6-34

[…] genus, if available. for genera with only a single representative named species, the second-largest genome from the same species was instead added to the set., genome trees were inferred using the fastme application, version 1.1 [] with default parameter settings. networks were constructed using the neighbor-net algorithm as implemented in version 4.11.3 of splitstree []. the "use weights" […]


To access a full list of citations, you will need to upgrade to our premium service.

FastME in publications

 (61)
PMCID: 5915733
PMID: 29691339
DOI: 10.1128/mBio.00573-18

[…] and snp number difference estimates are available in  in the supplemental material. finally, the matrix of evolutionary distances was used to infer a minimum-evolution phylogenetic tree with fastme v.2.1.5 (, )., in a specific experiment dedicated to determine the reproducibility of all parts of the sequencing process (from extraction to sequence analysis), single-spore isolation […]

PMCID: 5900718
PMID: 29421852
DOI: 10.1111/mec.14523

[…] & gascuel, ) and bootstrap analysis with 100 replicates (files  and ). the topology of the tree was confirmed by three additional methods. first, we used a neighbour‐joining approach in fastme 2.0 (lefort, desper, & gascuel, ) with the logdet substitution model and tree refinement by subtree pruning and regrafting (file ). second, we used the parsimony ratchet approach […]

PMCID: 5698912
PMID: 29188023
DOI: 10.5256/f1000research.13945.r27739

[…] genes; see associated data repository . using these single-copy orthogroups, gene trees were first constructed, then the species tree was inferred using the distance-based method implemented by fastme . the resultant species tree (see associated data repository ) exhibits strong congruence to the phytophthora phylogeny recently published by , providing more evidence that the genome assembly […]

PMCID: 5742155
PMID: 29312207
DOI: 10.3389/fmicb.2017.02501

[…] from the available geodermatophilaceae (and outgroup) whole proteome sequences using the high-throughput version () of the genome blast distance phylogeny (gbdp) approach () in conjunction with fastme () as described earlier (). an additional fastme tree was inferred without the two outgroup genomes to detect potential long-branch attraction to the outgroup, a process called long-branch […]

PMCID: 5673892
PMID: 29109526
DOI: 10.1038/s41467-017-01118-x

[…] cells (acinar, duct, alpha, and beta cells). phylogenetic trees were generated calculating euclidean distance matrices based on all cpg sites on the array by the minimal evolution method using the fastme.bal function from the r package ape., the bioconductor package conumee was used to calculate copy number alterations from the intensities obtained from the 450k array (bin probe size was set […]


To access a full list of publications, you will need to upgrade to our premium service.

FastME institution(s)
Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS & Université de Montpellier, France
FastME funding source(s)
Supported by the Institut Français de Bioinformatique (RENABI-IFB, Investissements d’Avenir).

FastME reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FastME