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showTree, a visualization tool for gene/protein families.

showTree can visualize the following files in a single figure:

  • a multiple sequence alignment (MSA)
  • a gene/protein tree in newick format
  • a protein domain annotation in Pfam_scan output format

The inputs above can be combined freely, e.g. you may provide any combination such as

  • tree + MSA + domains
  • tree + MSA
  • tree + domains
  • MSA + domains
  • ...

Requirements

showTree requires Python2.7 or Python3.4 or higher and the following Python packages:

  • ete3

pip install 'ete3==3.0.0b35'

  • Biopython

pip install biopython

It is absolutely crucial that you're using ete3 version 3.0.0b35 and not the latest version. The latest version simply won't work because some classes that showTree depends on were silently removed from ete3. The protein domain annotation must be in the output format of pfam_scan.pl which you can download here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ .

note for bornberglab-members who use calcTree (click to expand) The input files (MSA and gene tree) may also be computed with calcTree (https://ebbgit.uni-muenster.de/ckeme_01/geneSearch/wikis/calcTree). showTree can also parse the calcTree config file to automatically find the domain annotation of proteins in the MSA.

Usage

usage: showTree.py [-h] [-m MSA] [-t TREE]
                   [-d DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...]]
                   [-c CONFIG] [-g GFFS [GFFS ...]] [-o OUTPUT_PATH]
                   [-s SCALE_FACTOR] [-hl [HIGHLIGHT [HIGHLIGHT ...]]]
                   [-r ROOT] [-hn HIDE_NODES [HIDE_NODES ...]] [--lineseq]

optional arguments:
  -h, --help            show this help message and exit

main arguments:
  -m MSA, --msa MSA     Path to an untrimmed multiple sequence alignment in
                        FASTA format (the one produced by calcTree usually
                        ends with "_aln.fa")
  -t TREE, --tree TREE  Path to a gene tree, i.e. the best-scoring gene tree
                        with bootstrap values (not as branch labels) produced
                        by RAxML, usually the file name starts with
                        "RAxML_bipartitions."
  -d DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...], --domain_annotations DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...]
                        Path(s) to one or more Pfam_scan domain annotation(s)
                        of the proteins (standard method to display protein
                        domains)
  -c CONFIG, --config CONFIG
                        Path to the geneSearch/calcTree configuration file
                        (alternative method to display protein domains)

additional optional arguments:
  -g GFFS [GFFS ...], --gffs GFFS [GFFS ...]
                        Path to one or more GFF files containing CDS features
                        of the proteins. Used to mark intron positions. Only
                        works if the 9th (=last) column of the GFF contains
                        the protein IDs
  -o OUTPUT_PATH, --output_path OUTPUT_PATH
                        Path to the output image file. Must end with .PDF,
                        .PNG or .SVG. Tree will be shown in a window if
                        omitted
  -s SCALE_FACTOR, --scale_factor SCALE_FACTOR
                        Horizontal scaling factor of the MSA (default: 1.0).
                        Decrease this value if your image is too wide!
  -hl [HIGHLIGHT [HIGHLIGHT ...]], --highlight [HIGHLIGHT [HIGHLIGHT ...]]
                        Highlight specific clades or terminal nodes with a
                        background color. Comma-separated IDs will colour each
                        terminal node separately. Plus-separated IDs will
                        colour the whole clade that contains those IDs.
                        Example: --highlight red:prot01,prot02,prot03
                        green:prot04 lightyellow:prot05+prot06
  -r ROOT, --root ROOT  Set an outgroup node at which the tree will be rooted.
                        If multiple IDs are specified (plus-separated), the
                        whole clade that contains these IDs will be used for
                        rooting
  -hn HIDE_NODES [HIDE_NODES ...], --hide_nodes HIDE_NODES [HIDE_NODES ...]
                        Hide terminal nodes that contain the specified
                        substring; e.g. use "FBpp" to hide all Drosophila
                        proteins
  --lineseq             Draw a simple line instead of the amino acid /
                        nucleotide sequence

Example output

An example output tree that was generated with the command showTree -m ORTHO_ALL1421_aln.fa -d ORTHO_ALL1432.pfamscan -t RAxML_bipartitions.ORTHO_ALL1421_aln.tree -s 0.5 -o tree.pdf

example_tree