A couple of tools I made for post orthoMCL/orthAgogue down-stream analysis. The first tool computes a set of CSV files with presence/absence or 'count' information relating to your orthologue groups and taxa. The second tool allows you to take the output of a DOLLOP analysis along with the orthologue groups and plot them to locations on the tree topology as a list and set of alignments for each node. The final two scripts allow you to plot this information in a image created in R using ggtree.

Run this script to:

1. Collate all sequences from each ortholog group into separate FASTA files.
2. Generate a Presence Absense Grid
3. Is the taxa/genome represented in the ortholog group? 0 or 1
4. Also generates a transposed grid in a phylip-like format which is useful for Dollo Parsimony / ML analyses.
5. Generate Count (tally) Grid
6. How many representations (genes) are present in each ortholog groups? 0...n

You will need these files:

- from orthomcl: goodProteins.fasta
- from orthomcl: groups.txt
- from orthomcl: compliantFasta directory

You will need to convert the presence_absence_grid.csv file into a phylip-like format. To do this you must do four things:

1. transpose the data,
2. remove the first line (header information),
3. insert spaces between the 'taxa' names and 0/1s and
4. add number of taxa and number of 'sites' to the top of the file.

To do this:

 1. perl -F, -lane 'for ( 0 .. $#F ) { $rows[$_] .= $F[$_] }; eof && print map "$_\n", @rows' presence_absense_grid.csv > presence_absense_grid_transposed.csv
 2. perl -ni -e 'print unless $. == 1' presence_absense_grid_transposed.csv
 3. cp presence_absense_grid_transposed.csv presence_absense_grid.phy
 4. sed -i 's/\(\w\{4\}\)\(.*\)/\1      \t\2/g' presence_absense_grid.phy
 5. Open in your favourite text editor and add " XX YYYY", where XX = number of taxa, and YYYY = number of ortholog groups

Before running extract_dollop_output_sequences_v2-fast.pl you will need to run 'dollop' from the PHYLIP package. This requires the phylip-like file you created in the step above, and possibly a user-specified tree topology.

A program to take the "outfile" from a PHYLIP DOLLOP run and parse the output in to a more useful format. It requires at least two pieces of information:

1. the "outfile" from DOLLOP
2. the number of states being tested (i.e. number of orthologs)

For running with OrthoMCL data you will also need:

1. a list of orthogroup names (edit groups.txt accordingly)
2. a directory with the *.fasta sequences of each orthogroup (from the previous script)

The program outputs four different options:

1. A phylip-like output file, parsed from the state information in the "outfile" from dollop.
2. A tab-separated report listing the node and number of gain, loss and 'core' states in either of two styles:
3. 'New-style': This makes the node column one value, which is represented by a internal node number or leaf label. The number is the node number starting from '1' on the first leaf.
4. 'Old-style': This makes the node column into two values, corresponding to positions across the tree using the node values from the dollop outfile.
5. This outputs a directory, in the 'old-style' format (e.g. root__1 or 3__label), making a directory for each node transition along with three files. One each for loss, gain and core.
6. This copies the *.fasta files from a location for each of the lists in the previous directory, to their appropriate directory.

Mandatory Input:
	-i Dollop outfile
	-s Number of states (orthogroups)
	-o Output Directory
Other Options (one or all required):
outfile to phylip-like:
	-c Convert to Phylip-like File (not needed if using -p)
Report Tables:
	-n New-style Report (includes internal tree node numbers)
	-r Old-style report (between-nodes from dollop outfile)
Structured Lists:
	-l Lists of Core/Losses/Gains (requires -g)
	-g Ortholog Group List
	-p phylip-like file (unless -c)
Sequence Collation:
	-f Get .fasta files for groups from directory (requires -d)
	-d The *.fasta directory
	-n Nodes directory (unless -l)
	-x Exclude "core" marked ortholog groups
e.g. Equivalent: program.pl -i input -s number -o output -cr -l -g list.txt or program.pl -i input -s number -o output -rl -g list.txt -p phylip-like.phy

For the R script below to work your tree needs to have it's internal nodes labelled as well as the leafs. This will add numbers to all the internal nodes, you need to specifiy how many leafs nodes (i.e. taxa) you have.

Requires

1. ggplot2
2. ggtree
3. internally labelled tree
4. 'new-style' output from extract_dollop_output_sequences_v2-fast.pl