ETE-NPR

A portable application for Nested Phylogenetic Reconstruction and workflow design

For the next examples, you will need to download the following data files:

• p53.fasta
• NUP62.aa.fa
• NUP62.nt.fa

Basic gene-tree reconstruction example

• Execute a fast analysis:

  $ npr -a p53.fasta -o p53_results1 -w standard_fasttree 

  After a short time, your tree should be found in p53_results/, including (if graphics was available in your system) an image of your tree and alignment (Figure 2).

Gene-tree reconstruction using several workflows

• Workflows are specified using the -w parameter, and several strategies can be applied at once, thus recycling common tasks.

$ npr -a p53.fasta -o p53_results -w standard_fasttree standard_raxml

Recursive gene tree reconstruction

Note that recursive phylogenies are only recommended for very large trees or very patchy alignments. Next examples are kept small to avoid large computation times.

• Any workflow can be turned into recursive by ussing the --recursive option:

  $ npr -a p53.fasta -o p53_results3 -w standard_fasttree --recursive

  This command will execute the standard RAxML workflow for all the nodes in the resulting tree, meaning that alignment and model-selection steps will be optimized at each iteration.

• As this can be very intensive computationally, you may want to specify different workflows for different tree levels.

  $ npr -a p53.fasta -o p53_results4 -w standard_fasttree \
        --recursive "size-range:0-19,standard_raxml" "size-range:20-500,standard_fasttree"
  

  This command will execute the standard FastTree workflow for the first iteration, and for partitions of at least 20 sequences. Smaller partitions will be analyzed using RAxML.

Recursive gene tree reconstruction using mixed sequence types

• Recursive phylogenies allow to combine the use of nucleotide and amino-acid sequnece in the same tree. You just need to specify a nucleotide fasta file and your recursive strategy

  $ npr -a NUP62.aa.fa -n NUP62.nt.fa -o NUP62_results1 -w standard_fasttree \
        --recursive seq-sim-range:0.95-1,standard_fasttree --nt_switch_thr 0.95
  

  This command will execute the standard fasttree workflow using amino-acid sequences in the first iteration. Recursive refinement is done using the same workflow but will only occur in nodes whose sequence similarity (aa based) is higher than 0.95, which is also the threshold for switching to nucleotide alignments. Result is shown in Figure 3.

Fig 1. Standard output of a typical ETE-NPR analysis. Different tasks are monitored during execution. The verbosity of log messages can be controlled using the-v option.

Fig 2. An image of the final tree generated by ETE-NPR, including the schematic representation of the multiple sequence alignment.

Fig 3. Blue nodes represent nodes whose internal topology has been optimized with NPR. Green background show the parts of the phylogeny that were optimized using a codon based alignment.

For the next examples, you will need to download the following data files:

• cogs.txt
• proteome_seqs.fa

Basic super-matrix tree reconstruction

super-matrix based strategies require:

• A sumermatrix workflow defining how orthologous genes are selected and concatenated
• the genetree workflow specifiying how individual gene trees and alignments should be recunstructed prior to concatenation.
• A file containg all sequences in FASTA format, typically all proteomes or genomes
• and a text file grouping orthologous sequences, known as the Clusters of Orthologs Groups (COGs).

  The cogs file is text file containing a group of orthologous sequences per line, each sparated by TABs. In example:

  sp1_seqA   sp2_seqA    sp3_seqA
  sp1_seqB   sp2_seqB    sp3_seqB
  sp1_seqC   sp3_seqC    sp4_seqC    sp5_seqC
  ...
              

And a simple run using the above example fil would look like this:

$ npr -a proteome_seqs.fa --cogs cogs.txt -o sptree1_results/ -m sptree_dummy -w linsi_fasttree