The DOI matches its Crossref record.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Open accessAbstract
Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications. Contact: tgabaldon@crg.es
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Items 201–209 of 209
Ishii, Y., Kanamori, S., Deguchi, R., Kawata, M., Maruyama, S., Yoshida, T., & Kamikawa, R. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf133 · Cited by 2
Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair, P. O., Pennati, A., Herrera-Ubeda, C., & Holland, P. W. H. (2025) · Current Biology · doi:10.1016/j.cub.2025.09.051 · Cited by 2
Coral anthozoan-specific opsins employ a novel chloride counterion for spectral tuning
Sakai, Y., Sen, S., Sugihara, T., Kakeyama, Y., Iwasaki, M., Schertler, G. F., Deupi, X., Koyanagi, M., & Terakita, A. (2025) · eLife · doi:10.7554/elife.105451 · Cited by 2
Vidovszky, M. Z., Kaján, G. L., Böszörményi, K. P., Podgorski, I. I., Doszpoly, A., Ballmann, M. Z., Mitró, G., Skoda, G., Turk, M., Groothuizen, M. K., et al. (2025) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2025.108287 · Cited by 1
Hamilton, R., Gebbie, W., Bowman, C., Mantanona, A., & Kalyuzhnaya, M. G. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.01364-24 · Cited by 1
Ramaprasad, A., Burda, P.-C., Calvani, E., Sait, A., Palma-Duran, S. A., Withers-Martinez, C., Hackett, F., MacRae, J., Collinson, L., Gilberger, T.-W., et al. (2022) · doi:10.1101/2022.06.14.496138 · Cited by 1
Caspase-1 activates gasdermin A in non-mammals
Billman, Z. P., Kovacs, S. B., Wei, B., Kang, K., Cissé, O. H., & Miao, E. A. (2024) · doi:10.7554/elife.92362.3 · Cited by 1
Li, X., He, Z., Liu, A., Meng, F., Zhang, X., Li, N., Liu, H., Lu, Y., Wu, Z., Fan, H., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-09523-z · Cited by 1
PWO proteins are associated with PRC2 since their emergence in vascular plants
Khan, A., Haider, S., Sharaf, A., Kusová, A., Skalák, J., Jourdain, C., Rennie, M., Schrumpfová, P. P., Hejátko, J., Schubert, D., et al. (2025) · doi:10.1101/2025.03.15.643013 · Cited by 1
Metadata
- Authors
- Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-08
- Volume
- 25
- Issue
- 15
- Pages
- 1972-1973
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2115888213
- Cited by
- 12,751
- References
- 0
- FWCI
- 12.96
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
