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raxmlGUI specifications


Unique identifier OMICS_26717
Name raxmlGUI
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Medium
Version 1.5b1
Stability Stable
Maintained Yes


No version available



  • person_outline raxml Team
  • person_outline Daniele Silvestro
  • person_outline Ingo Michalak

Additional information


Publication for raxmlGUI

raxmlGUI citations


Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Sci Rep
PMCID: 5910433
PMID: 29679020
DOI: 10.1038/s41598-018-24686-4

[…] ollowing the classification of Verma et al., we categorized the proteins into main groups of aquaporins: AQP, AQGP and its subgroup XIP. Maximum Likelihood analysis of aquaporins was carried out with raxmlGUI v. 1.3 running RAxML 8.1.3 and ML bootstrap analysis with 1,000 replicates. The phylogenetic tree was visualized and edited using MEGA6. […]


Evolving in the highlands: the case of the Neotropical Lerma live bearing Poeciliopsis infans (Woolman, 1894) (Cyprinodontiformes: Poeciliidae) in Central Mexico

BMC Evol Biol
PMCID: 5910627
PMID: 29678141
DOI: 10.1186/s12862-018-1172-7

[…] red the best partition by assigning substitution models for each gene. The parameters of each model are provided in Additional file .Gene trees were constructed with Maximum Likelihood implemented in RAxMLGUI v.1.3.1 [, ], using the substitution model implemented for each gene. The GTR + G + I [] substitution model was used for the concatenated genes matrix and 10,000 bootstrap replicates with the […]


DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

PLoS One
PMCID: 5901997
PMID: 29659610
DOI: 10.1371/journal.pone.0195770
call_split See protocol

[…] aligned with all the rbcL sequences in the R-Syst::diatom library using Muscle [] in Seaview []. The best substitution model was then tested in MEGA7 []. A constraint phylogeny was then calculated in raxmlGUI [] using the fast tree search option. The constraint sequences were the turtle OTUs sequences and the shortest sequences of R-Syst::diatom library. A tree was drawn using the online tool iTOL […]


Multiple Origins and Nested Cycles of Hybridization Result in High Tetraploid Diversity in the Monocot Prospero

Front Plant Sci
PMCID: 5932365
PMID: 29755483
DOI: 10.3389/fpls.2018.00433
call_split See protocol

[…] tion replicates holding maximally 10 trees per replicate, SPR branch swapping, and MulTrees on.Maximum likelihood (ML) analyses were conducted for ITS and the concatenated three plastid regions using raxmlGUI 1.3 (Silvestro and Michalak, ) with the GTR+GAMMA nucleotide substitution model. The ML tree and BS for each region were obtained using the rapid bootstrap algorithm (Stamatakis et al., ) wit […]


Deep intraspecific DNA barcode splits and hybridisation in the Udea alpinalis group (Insecta, Lepidoptera, Crambidae) – an integrative revision

PMCID: 5904419
PMID: 29674896
DOI: 10.3897/zookeys.746.22020
call_split See protocol

[…] ad 1000 thermal cycler; ExoSAP clean-up was done on a MJ Research PTC-200 thermal cycler.The three gene datasets (COI, Wingless, EF1a) were aligned with PhyDE 0.9971 () and analysed individually with raxmlGUI v. 1.5b2 (; ), using a Maximum Likelihood (ML) search under the GTRGAMMA model () and with a thorough bootstrap of 1,000 Bootstrap replicates. Phylograms were edited in TreeGraph version 2.13 […]


Longitudinal study of age specific pattern of coronavirus infection in Lyle’s flying fox (Pteropus lylei) in Thailand

Virol J
PMCID: 5819653
PMID: 29463282
DOI: 10.1186/s12985-018-0950-6
call_split See protocol

[…] ourier Transform (MAFFT) []. Phylogenetic trees were created based on 357 and 299 bp RdRp gene sequence using the maximum likelihood method. Bootstrap values were determined using 1000 replicates via RaxmlGUI 1.3 with outgroup (Bulbul CoV/HKU11–934/Pycnonotus jocosus/CHN/2007/FJ376619) using the GTRI substitution model []. The phylogenetic tree was visualised using the FigTree program, version 1.4 […]


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raxmlGUI institution(s)
Department of Botany and Molecular Evolution, Research Institute Senckenberg, Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany; Department of Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
raxmlGUI funding source(s)
Supported by the German Research Foundation (DFG, projects ZI 557/6-2, ZI 557/7-1, SCHU 2426/1-1, SCHU 2426/2-2), and the research funding programme “LOEWE Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research, and the Arts.

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