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Protocols

trimAl specifications

Information


Unique identifier OMICS_08062
Name trimAl
Alternative name Phylemon web server
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.4
Stability Beta
Maintained Yes

Subtool


  • readAl

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Versioning


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Maintainer


  • person_outline Toni Gabaldón

Information


Unique identifier OMICS_08062
Name trimAl
Alternative name Phylemon web server
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Version 1.4
Stability Beta
Maintained Yes

Subtool


  • readAl

Maintainer


  • person_outline Toni Gabaldón

Publication for trimAl

trimAl citations

 (562)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] ellales homologues retrieved as described above was used for phylogenomic analyses. Multiple-sequence alignment was performed using MUSCLE v3.6 (). Gaps and poorly aligned regions were excluded using trimAl v1.4 (). Aligned protein sequences that were longer than 50 amino acids (1,241 of the 1,280 homologues) were selected using a Python script (“Filter_Len.py”; available from GitHub) and then con […]

library_books

Genome wide expert annotation of the epigenetic machinery of the plant parasitic nematodes Meloidogyne spp., with a focus on the asexually reproducing species

2018
BMC Genomics
PMCID: 5934874
PMID: 29724186
DOI: 10.1186/s12864-018-4686-x

[…] as the fourth step. Putative epigenetic factors protein sequences were aligned by MAFFT version 7.245 [] with --auto option. The alignment was manually checked to remove misaligned sequences. We used trimAl version 1.2 [] to remove gap-rich columns in the multiple alignments. Maximum likelihood trees were built with RAxML version 8.1 [] with an automatic detection of the fittest evolutionary model […]

call_split

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2
call_split See protocol

[…] ofinder v2.1.2 [], with initial search results filtered to retain only groups with an e-value <1e-30. Sequences from each of the 654 orthologous groups were aligned and trimmed using MAFFT v7.310 and trimAl v1.3 [, ] as described previously [] with the following alterations. Sequence alignments were trimmed using the nogaps automated option and two orthologous groups were removed from the final an […]

library_books

Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

2018
PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] protein trees (Figs and and ), OCTIN sequences from the NCBI reference protein database were used. MAFFT [] with the option E-INS-i was used to obtain sequence alignments, which were trimmed using Trimal [] at a gap threshold of 70%. ML bootstrap analysis was performed with RAxML [] using the automatic bootstrapping option [] (300 replicates) and the PROTGAMMAILGX model as suggested by ProtTest […]

library_books

Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

2018
BMC Genomics
PMCID: 5937819
PMID: 29690866
DOI: 10.1186/s12864-018-4683-0

[…] defined as a gene family that only contains a single copy in each of the 72 species. Multiple sequence alignments were generated using MUSCLE []. The poorly aligned regions were further trimmed using trimAl v1.2 []. A maximum likelihood (ML) analysis was performed for each of the 160 orthologous groups using RAxML v8.2.10 with 100 bootstrap replicates [] under PROTGAMMAIJTTF model as recommended b […]

call_split

The role of retinoic acid signaling in starfish metamorphosis

2018
PMCID: 5910596
PMID: 29721256
DOI: 10.1186/s13227-018-0098-x
call_split See protocol

[…] re shown in Additional file : Table S1 and aligned using MAFFT ver. 7 (https://mafft.cbrc.jp/alignment/server/) with the default parameters []. Amino acid sites for tree construction were selected by trimAl using a gap threshold value of 0.8 []. A best-fitting amino acid substitution model and a maximum likelihood tree were inferred using RAxML 8.2.0 []. Confidence values were calculated after 100 […]

Citations

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trimAl institution(s)
Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr Aiguader, Barcelona, Spain
trimAl funding source(s)
FIS (06-213 to T.G.) and MEC (GEN2006-27784-E/PAT to T.G.)

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