BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees

Bond, Stephen R.; Keat, Karl; Barreira, Sofia N; Baxevanis, Andreas D

doi:10.1093/molbev/msx089

Cited by 8 publications

(6 citation statements)

References 18 publications

(5 reference statements)

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“…The resulting alignments frequently contained indel‐rich stretches of poorly aligned non‐exonic sequences which were several thousand base pairs long. We used BuddySuite v1.3.0 (Bond et al, 2017 ) to reduce the number of these regions by trimming alignment positions that consisted of more than 50% gaps. Any alignments that were missing more than 20% of the samples or the S. hirsuta sample were also excluded from further analysis.…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

Gerschwitz-Eidt

Dillenberger

Kadereit

2023

Ecology and Evolution

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Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA‐sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae . Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well‐known refugia. We hypothesize that low light requirements evolved when species persisting in cold‐stage refugia were forced into marginal habitats by more competitive warm‐stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.

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Section: Methodsmentioning

confidence: 99%

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

Gerschwitz-Eidt

Dillenberger

Kadereit

2023

Ecology and Evolution

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“…Ape ( 12 ) is a package dedicated to the analyses of phylogenetics and evolution in the R language. Buddy Suite ( 13 ) is another python framework (command line) to manipulate phylogenetic trees and alignments. BIO++ ( 14 ) is a C++ library for the analysis of sequences and trees.…”

Section: Introductionmentioning

confidence: 99%

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Lemoine

Gascuel

2021

NAR Genomics and Bioinformatics

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Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https://github.com/evolbioinfo/gotree, Bioconda and DockerHub.

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“…Another advanced feature of PhySpeTree is the fully optimized configuration of software streams. We then compared the run time of tree building in PhySpeTree with that of a pipeline in BuddySuit [9]. The same third-party software and parameters were used.…”

Section: Resultsmentioning

confidence: 99%

“…Toolkits and pipelines have been developed for phylogenetic reconstruction (Table 1). Toolkits such as BuddySuite [9], ETE3 [10], and MEGA [11] are widely used for phylogenetic inference and tree manipulation. BuddySuite and ETE3 provide rich interfaces that allow researchers to carry out secondary development.…”

Section: Introductionmentioning

confidence: 99%

PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

et al. 2019

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BackgroundPhylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building.ResultsHere, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree.ConclusionsTogether with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).

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BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees

Cited by 8 publications

References 18 publications

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

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