Applications and considerations of GToTree: a user-friendly workflow for phylogenomics
MD Lee - Evolutionary Bioinformatics, 2019 - journals.sagepub.com
Phylogenomics is the practice of attempting to infer evolutionary relationships at a genome-
level. This is becoming a standard step in the characterization of newly recovered genomes …
level. This is becoming a standard step in the characterization of newly recovered genomes …
[PDF][PDF] Construction of a phylogenetic matrix: Scripts and guidelines for phylogenomics
Phylogenomics is a new field that infers evolutionary relationships of taxa at the genome-
scale level. The increment of molecular data may raise the potential bias as the limiting …
scale level. The increment of molecular data may raise the potential bias as the limiting …
[HTML][HTML] Agalma: an automated phylogenomics workflow
Background In the past decade, transcriptome data have become an important component
of many phylogenetic studies. They are a cost-effective source of protein-coding gene …
of many phylogenetic studies. They are a cost-effective source of protein-coding gene …
To what extent current limits of phylogenomics can be overcome?
Current phylogenomic methods are still a long way from implementing a realistic genome
evolution model. An ideal approach would require a general joint analysis of genomic …
evolution model. An ideal approach would require a general joint analysis of genomic …
A Guide to Phylogenomic Inference
JSL Patané, J Martins Jr, JC Setubal - Comparative Genomics: Methods …, 2024 - Springer
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. Phylogenomics has significant …
account whole genomes or large fractions of genomes. Phylogenomics has significant …
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
L Guy - Bioinformatics, 2017 - academic.oup.com
With the wealth of available genome sequences, a difficult and tedious part of inferring
phylogenomic trees is now to select genomes with an appropriate taxon density in the …
phylogenomic trees is now to select genomes with an appropriate taxon density in the …
Phylogenomics: evolution and genomics intersection
VS Gomase, S Tagore - International Journal of …, 2009 - inderscienceonline.com
Phylogenomics is the analysis of genomes of a group of closely related species. Almost all
functional prediction methods rely on the identification, characterisation and quantification of …
functional prediction methods rely on the identification, characterisation and quantification of …
A practical guide to design and assess a phylogenomic study
J Lozano-Fernandez - Genome Biology and Evolution, 2022 - academic.oup.com
Over the last decade, molecular systematics has undergone a change of paradigm as high-
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
Phylogenomics
MJ Telford - Current Biology, 2007 - cell.com
What is meant by 'phylogenomics'? I'm afraid it depends rather on whom you ask: The
majority of recent papers referring to phylogenomics are studies using large sets of …
majority of recent papers referring to phylogenomics are studies using large sets of …
Co-phylog: an assembly-free phylogenomic approach for closely related organisms
With the advent of high-throughput sequencing technologies, the rapid generation and
accumulation of large amounts of sequencing data pose an insurmountable demand for …
accumulation of large amounts of sequencing data pose an insurmountable demand for …