#### README ####

Please send comments or questions to http://lists.ensembl.org/mailman/listinfo/dev.

----------------------------------------------
Multiple Alignment Format (MAF) FLATFILE DUMPS
----------------------------------------------
This directory contains Compara MAF flatfile dumps.  To ease
downloading of the files, an MAF file is created for each chromosome.
All files are then compacted with GNU Zip for storage efficiency.

----------
FILE NAMES
----------
The files are consistently named following this pattern:
<species>.<assembly>.<release>.<data type>.<region>.maf.gz

EXAMPLE MAF whole-genome multiple alignment (compara) data file names
Compara.pecan_7_way.chr13_1.maf.gz
Compara.pecan_gerp_10_way.chr3_5.maf.gz
Compara.pecan_gerp_10_way.others_1.maf.gz

-----------
FILE FORMAT
-----------

The MAF format specification can be found on the UCSC website: https://genome.ucsc.edu/FAQ/FAQformat.html#format5

We add extra information in the form of comments

a) Description of "composite" sequences
# epo2x composite sequence: mesocricetus_auratus KB708322.1_11360002442546 is: scaffold:MesAur1.0:KB708322.1:593611:593796:1 + scaffold:MesAur1.0:KB708322.1:594574:595896:1

In EPO_EXTENDED alignments, we sometimes concatenate the scaffolds of
some species and consider the result as a single sequence that is aligned
to the other species. We name these sequences "composite" and we list at
the top of the section the list of underlying scaffolds they are made of.

b) the tree linking the various sequences (in Newick format)
# tree: (Hsap_11_134959233_135017027[-]:0.00825809999999999,Ggor_11_135146106_135206808[-]:0.008760400000000002)Aseq_Ancestor_1102_1085092_1_57552[+]:0.007914300000000013;

The node names follow the pattern: "species_chromosome_start_end[strand]",
with Ensembl-style coordinates, i.e. 1-based regardless of the orientation.

Also note that for EPO alignments, the sequences are listed following an
in-order traversal of the tree (i.e. child1_subtree, node, child2_subtree),
whereas the Newick format is basically a post-order traversal of the tree.

c) conservation scores
# gerp scores: 0.74 0.74 -0.36 -0.33 0.74 -0.45

This is the list of the GERP conservation score computed for each position of the alignment

-------------------
GENOMIC COORDINATES
-------------------

The coordinates shown in the "s" lines follow the MAF convention, i.e.:
> This is a zero-based number. If the strand field is "-" then this is the
> start relative to the reverse-complemented source sequence

For instance, "Ppan_11_133841373_133858123[+]" (the name of the sequence in
the tree) corresponds to the sequence header "pan_paniscus.11 133841372 16751 + 134183262":
 - [it's on the positive strand]
 - 133841372=133841373-1
 - 16751=133858123-133841373+1
"Mspr_9_24484589_24506699[-]" corresponds to "mus_spretus_spreteij.9 101742604 22111 - 126249303":
 - [it's on the negative strand]
 - 126249303 is the length of the chromosome
 - 101742604=126249303-24506699
 - 22111=24506699-24484589+1