ArticleGigaScience2019
Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- An ubiquitous antibacterial toxin from human gut bacteria engenders neonatal colonization advantage.Nature communications · 2026Article
- Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.PloS one · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Phylogenies from unaligned proteomes using sequence environments of amino acid residues.Scientific reports · 2022Article
- Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin.Frontiers in microbiology · 2022Article
- The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design.Scientific reports · 2021Article
- App-SpaM: phylogenetic placement of short reads without sequence alignment.Bioinformatics advances · 2021Article
- Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- SWeeP: representing large biological sequences datasets in compact vectors.Scientific reports · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
- Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.BMC bioinformatics · 2019Article
- Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast.Pathogens (Basel, Switzerland) · 2019Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.GigaScience · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Word-based or 'alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Here, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.