Skip to content
naulon
Get started

No retraction, correction or concern found when last checked on Oct 26, 2026.

Agalma: an automated phylogenomics workflow

Casey W Dunn, Mark Howison, Felipe Zapata

BMC Bioinformatics · 2013

doi:10.1186/1471-2105-14-330

Abstract

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 sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies.

Results. We present Agalma, an automated tool that constructs matrices for phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma.

Conclusions. Agalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended. Agalma also facilitates methods development by providing a complete modular workflow, bundled with test data, that will allow further optimization of each step in the context of a full phylogenomic analysis.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

Read at PubMed Central

References 31

  1. 1.

    Dunn CW Hejnol A Matus DQ Pang K Browne WE Smith SA Seaver E Rouse GW Obst M Edgecombe GD Sørensen MV Haddock SHD Schmidt-Rhaesa A Okusu A Kristensen RM Wheeler WC Martindale MQ Giribet G Broad phylogenomic sampling improves resolution of the animal tree of lifeNature2008 4527188745749[http://dx.doi.org/10.1038/nature06614]

    Not in our library10.1038/nature06614

  2. 2.

    Hejnol A Obst M Stamatakis A Ott M Rouse GW Edgecombe GD Martinez P Baguñà J Bailly X Jondelius U Wiens M Müller WEG Seaver E Wheeler WC Martindale MQ Giribet G Dunn CW Assessing the root of bilaterian animals with scalable phylogenomic methodsProc R Soc B2009 276167742614270

    Not in our library10.1098/rspb.2009.0896

  3. 3.

    Smith SA Wilson NG Goetz FE Feehery C Andrade SCS Rouse GW Giribet G Dunn CW Resolving the evolutionary relationships of molluscs with phylogenomic toolsNature2011 4807377364367

    Not in our library10.1038/nature10526

  4. 4.

    Philippe H Derelle R Lopez P Pick K Borchiellini C Boury-Esnault N Vacelet J Renard E Houliston E QuEinnec E Da Silva C Wincker P Le Guyader H Leys S Jackson DJ Schreiber F Erpenbeck D Morgenstern B WOrheide G Manuel M Phylogenomics Revives Traditional Views on Deep Animal RelationshipsCurr Biol: CB2009 198706712[http://dx.doi.org/10.1016/j.cub.2009.02.052]

    Not in our library10.1016/j.cub.2009.02.052

  5. 5.

    Delsuc F Brinkmann H Chourrout D Philippe H Tunicates and not cephalochordates are the closest living relatives of vertebratesNature2006 4397079965968[http://www.nature.com/doifinder/10.1038/nature04336]

    Not in our library10.1038/nature04336

  6. 6.

    Sanderson MJ Phylogenetic Signal in the Eukaryotic Tree of LifeSci (New York, N.Y.)2008 3215885121123[http://www.sciencemag.org/cgi/doi/10.1126/science.1154449]

    Not in our library10.1126/science.1154449

  7. 7.

    Philippe H Telford MJ Large-scale sequencing and the new animal phylogenyTrends Ecol Evol2006 2111614620[http://dx.doi.org/10.1016/j.tree.2006.08.004]

    Not in our library10.1016/j.tree.2006.08.004

  8. 8.

    Edgecombe GD Giribet G Dunn CW Hejnol A Kristensen RM Neves RC Rouse GW Worsaae K Sørensen MV Higher-level metazoan relationships: recent progress and remaining questionsOrg Divers Evol2011 112151172[http://www.springerlink.com/index/10.1007/s13127-011-0044-4]

    Not in our library10.1007/s13127-011-0044-4

  9. 9.

    Parkinson J Anthony A Wasmuth J Schmid R Hedley A Blaxter M PartiGene–constructing partial genomesBioinformatics (Oxford, England)2004 20913981404[http://dx.doi.org/10.1093/bioinformatics/bth101]

    Not in our library10.1093/bioinformatics/bth101

  10. 10.
    SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics · 2007
    No notice
  11. 11.

    Howison M Dunn CW Sinnott-Armstrong NA BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenanceProceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP ’12)14–15 June 2012 Boston, MA, USAhttps://www.usenix.org/system/files/conference/tapp12/tapp12-final5.pdf

    Not in our library

  12. 12.

    Cock PJA Antao T Chang JT Chapman BA Cox CJ Dalke A Friedberg I Hamelryck T Kauff F Wilczynski B Hoon MJLd Biopython: freely available Python tools for computational molecular biology and bioinformaticsBioinformatics2009 251114221423[http://bioinformatics.oxfordjournals.org/content/25/11/1422] [PMID: 19304878]

    Not in our library10.1093/bioinformatics/btp163

  13. 13.

    Langmead B Salzberg SL Fast gapped-read alignment with Bowtie 2Nat Methods2012 94357359[http://www.nature.com/doifinder/10.1038/nmeth.1923]

    Not in our library10.1038/nmeth.1923

  14. 14.

    Grabherr MG Haas BJ Yassour M Levin JZ Thompson DA Amit I Adiconis X Fan L Raychowdhury R Zeng Q Chen Z Mauceli E Hacohen N Gnirke A Rhind N di Palma F Birren BW Nusbaum C Lindblad-Toh K Friedman N Regev A Full-length transcriptome assembly from RNA-Seq data without a reference genomeNat Biotechnol2011, [http://www.nature.com/doifinder/10.1038/nbt.1883]

    Not in our library10.1038/nbt.1883

  15. 15.

    Andrews S FastQC: A quality control tool for high throughput sequence data[http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/]

    Not in our library

  16. 16.

    Grabherr MG Haas BJ Yassour M Levin JZ Thompson DA Amit I Adiconis X Fan L Raychowdhury R Zeng Q Chen Z Mauceli E Hacohen N Gnirke A Rhind N di Palma F Birren BW Nusbaum C Lindblad-Toh K Friedman N Regev A Full-length transcriptome assembly from RNA-Seq data without a reference genomeNat Biotech2011 297644652

    Not in our library10.1038/nbt.1883

  17. 17.

    Tange O GNU Parallel: the command-line power toolLogin2011 364247[https://www.usenix.org/publications/login/february-2011-volume-36-number-1/gnu-parallel-command-line-power-tool]

    Not in our library

  18. 18.
    RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome · 2011
    No notice
  19. 19.

    Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein familiesNucleic Acids Research2002 30715751584[http://dx.doi.org/10.1093/nar/30.7.1575]

    Not in our library10.1093/nar/30.7.1575

  20. 20.
    MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons · 2011
    No notice
  21. 21.

    Talavera G Castresana J Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignmentsSyst Biol2007 564564577

    Not in our library10.1080/10635150701472164

  22. 22.

    Stamatakis A RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics (Oxford, England)2006 222126882690

    Not in our library10.1093/bioinformatics/btl446

  23. 23.

    Salichos L Rokas A Inferring ancient divergences requires genes with strong phylogenetic signalsNature2013 4977449327331[http://dx.doi.org/10.1038/nature12130]

    Not in our library10.1038/nature12130

  24. 24.

    Hejnol A Obst M Stamatakis A Ott M Rouse GW Edgecombe GD Martinez P Baguñà J Bailly X Jondelius U Wiens M Müller WEG Seaver E Wheeler WC Martindale MQ Giribet G Dunn CW Assessing the root of bilaterian animals with scalable phylogenomic methodsProc Biol Sci / R Soc2009 276167742614270[http://dx.doi.org/10.1098/rspb.2009.0896]

    Not in our library10.1098/rspb.2009.0896

  25. 25.

    Sukumaran J Holder MT DendroPy: a Python library for phylogenetic computingBioinformatics2010 261215691571[http://bioinformatics.oxfordjournals.org/content/26/12/1569]

    Not in our library10.1093/bioinformatics/btq228

  26. 26.

    Boussau B Szollosi GJ Duret L Gouy M Tannier E Daubin V Genome-scale coestimation of species and gene treesGenome Res2013 232323330[http://genome.cshlp.org/cgi/doi/10.1101/gr.141978.112]

    Not in our library10.1101/gr.141978.112

  27. 27.

    Putnam NH Srivastava M Hellsten U Dirks B Chapman J Salamov A Terry A Shapiro H Lindquist E Kapitonov VV Jurka J Genikhovich G Grigoriev IV Lucas SM Steele RE Technau U Martindale MQ Rokhsar DS FINNERTY JRSea anemone genome reveals ancestral Eumetazoan gene repertoire and genomic organizationSci (New York, N.Y.)2007 31758348694[http://www.sciencemag.org/cgi/doi/10.1126/science.1139158]

    Not in our library10.1126/science.1139158

  28. 28.

    Chapman JA Kirkness EF Simakov O Hampson SE Mitros T Weinmaier T Rattei T Balasubramanian PG Borman J Busam D Disbennett K Pfannkoch C Sumin N Sutton GG Viswanathan LD Walenz B Goodstein DM Hellsten U Kawashima T Prochnik SE Putnam NH Shu S Blumberg B Dana CE Gee L Kibler DF Law L Lindgens D Martinez DE Peng J The dynamic genome of HydraNature2010 4647288592596[http://dx.doi.org/10.1038/nature08830]

    Not in our library10.1038/nature08830

  29. 29.

    Dunn C Pugh P Haddock S Molecular Phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specializationSyst Biol2005 546916935[http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150500354837]

    Not in our library10.1080/10635150500354837

  30. 30.
    Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes · 2007
    No notice
  31. 31.
    Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs · 2013
    No notice

Cited by papers we hold 5

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.