Cookbook index

Using manual alignments

This recipe shows how run a phylogenetic workflow ignoring the sequence alignment phase. This allows to treat the input sequences as aligned sequences, and being used as it in next steps.

Requirements

Recipe

The only required step to use manual alignments is to set to none the alignining task in your preferred workflow name.

For instance, the following run, will run modeltesting and a raxml tree over a pre-aligned set of sequences:

In [2]:
%%bash 
ete3 build -a data/P53.alg.fa -w none-none-pmodeltest_soft_ultrafast-raxml_default -o manual_alg --clearall

Toolchain path: /Users/jhc/anaconda/bin/ete3_apps 
Toolchain version: 2.0.3


      --------------------------------------------------------------------------------
                  ETE build - reproducible phylogenetic workflows 
                                    unknown, unknown.

      If you use ETE in a published work, please cite:

        Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python
        Environment for Tree Exploration. BMC Bioinformatics 2010,
        11:24. doi:10.1186/1471-2105-11-24

      (Note that a list of the external programs used to complete all necessary
      computations will be also shown after execution. Those programs should
      also be cited.)
      --------------------------------------------------------------------------------

    
INFO -  Testing x86-64  portable applications...
       clustalo: OK - 1.2.1
Dialign-tx not supported in OS X
       fasttree: OK - FastTree Version 2.1.8 Double precision (No SSE3), OpenMP (1 threads)
         kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
          mafft: OK - MAFFT v6.861b (2011/09/24)
         muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar
          phyml: OK - . This is PhyML version 20160115.
     pmodeltest: OK - pmodeltest.py v1.4
          prank: OK - prank v.100802. Minimal usage: 'prank sequence_file'
       probcons: OK - PROBCONS version 1.12 - align multiple protein sequences and print to standard output
          raxml: OK - This is RAxML version 8.1.20 released by Alexandros Stamatakis on April 18 2015.
 raxml-pthreads: OK - This is RAxML version 8.1.20 released by Alexandros Stamatakis on April 18 2015.
         readal: OK - readAl v1.4.rev6 build[2012-02-02]
         statal: OK - statAl v1.4.rev6 build[2012-02-02]
        tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
         trimal: OK - trimAl v1.4.rev6 build[2012-02-02]
INFO -  Starting ETE-build execution at Mon Feb  8 14:17:42 2016
INFO -  Output directory /Users/jhc/_Devel/cookbook/recipes/manual_alg
INFO -  Erasing all existing npr data...
WRNG -  Using existing dir: /Users/jhc/_Devel/cookbook/recipes/manual_alg/db
INFO -  Reading aa sequences from data/P53.alg.fa...
WRNG -  8 target sequences
INFO -  ETE build starts now!
INFO -   Updating tasks status: (Mon Feb  8 14:17:42 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) MultiSeqTask (8 aa seqs, MSF, /none-none-...ml_default)
INFO -   (D) MultiSeqTask (8 aa seqs, MSF, /none-none-...ml_default)
WRNG -          Skipping alignment phase, using original sequences
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:44 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) AlgTask (8 aa seqs, ManualAlg, /none-none-...ml_default)
INFO -   (D) AlgTask (8 aa seqs, ManualAlg, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:46 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) ModelTesterTask (8 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:48 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) ModelTesterTask (8 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:50 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (R) ModelTesterTask (8 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /none-none-...ml_default)
INFO -   (D) ModelTesterTask (8 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:52 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:54 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:56 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (Q) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:17:58 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:18:00 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (Q) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -   (D) TreeTask (8 aa seqs, RaxML, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -   Updating tasks status: (Mon Feb  8 14:18:02 2016)
INFO -  Thread none-none-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 8
INFO -   (W) TreeMergeTask (8 aa seqs, TreeMerger, /none-none-...ml_default)
INFO -   (D) TreeMergeTask (8 aa seqs, TreeMerger, /none-none-...ml_default)
INFO -  Waiting 2 seconds
INFO -  Assembling final tree...
INFO -  Done thread none-none-pmodeltest_soft_ultrafast-raxml_default in 1 iteration(s)
INFO -  Writing final tree for none-none-pmodeltest_soft_ultrafast-raxml_default
   /Users/jhc/_Devel/cookbook/recipes/manual_alg/none-none-pmodeltest_soft_ultrafast-raxml_default/P53.alg.fa.final_tree.nw
   /Users/jhc/_Devel/cookbook/recipes/manual_alg/none-none-pmodeltest_soft_ultrafast-raxml_default/P53.alg.fa.final_tree.nwx (newick extended)
INFO -  Writing final tree alignment none-none-pmodeltest_soft_ultrafast-raxml_default
   /Users/jhc/_Devel/cookbook/recipes/manual_alg/none-none-pmodeltest_soft_ultrafast-raxml_default/P53.alg.fa.final_tree.used_alg.fa
INFO -  Writing root node alignment none-none-pmodeltest_soft_ultrafast-raxml_default
   /Users/jhc/_Devel/cookbook/recipes/manual_alg/none-none-pmodeltest_soft_ultrafast-raxml_default/P53.alg.fa.final_tree.fa
INFO -  Generating tree image for none-none-pmodeltest_soft_ultrafast-raxml_default
   /Users/jhc/_Devel/cookbook/recipes/manual_alg/none-none-pmodeltest_soft_ultrafast-raxml_default/P53.alg.fa.final_tree.png
INFO -  Done
INFO -  Deleting temporal data...
   ========================================================================
         The following published software and/or methods were used.        
               *** Please, do not forget to cite them! ***                 
   ========================================================================
   Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New
      algorithms and methods to estimate maximum-likelihood phylogenies:
      assessing the performance of PhyML 3.0. Syst Biol. 2010
      May;59(3):307-21.
   Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree
      Exploration. BMC Bioinformatics. 2010 Jan 13;11:24.
   Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and
      post-analysis of large phylogenies Bioinformatics (2014) 30 (9):
      1312-1313.