This directory contains all the 21-way Enredo-Pecan-Ortheus (EPO) multiple alignments corresponding
to Release 114 of Ensembl (see http://www.ensembl.org for further details and credits about the
Ensembl project).

The set of species is:
 - Norway rat - BN/NHsdMcwi (GRCr8)
 - Ryukyu mouse (CAROLI_EIJ_v1.1)
 - Western wild mouse (SPRET_EiJ_v3)
 - Mouse PWK/PhJ (PWK_PhJ_v3)
 - Mouse LP/J (LP_J_v3)
 - Mouse 129S1/SvImJ (129S1_SvImJ_v3)
 - Mouse WSB/EiJ (WSB_EiJ_v3)
 - Mouse (GRCm39)
 - Mouse C57BL/6NJ (C57BL_6NJ_v3)
 - Mouse NZO/HlLtJ (NZO_HlLtJ_v3)
 - Mouse BALB/cJ (BALB_cJ_v3)
 - Mouse NOD/ShiLtJ (NOD_ShiLtJ_v3)
 - Mouse A/J (A_J_v3)
 - Mouse CBA/J (CBA_J_v3)
 - Mouse C3H/HeJ (C3H_HeJ_v3)
 - Mouse DBA/2J (DBA_2J_v3)
 - Mouse AKR/J (AKR_J_v3)
 - Mouse FVB/NJ (FVB_NJ_v3)
 - Mouse CAST/EiJ (CAST_EiJ_v3)
 - Steppe mouse (MUSP714)
 - Shrew mouse (PAHARI_EIJ_v1.1)

The species tree was:
(
(
  (
    (
      (
        (
          (
            (
              (
                (
                  (
                    (
                      (
                        (
                          (
                            Mus musculus strain C3H/HeJ:0.00023,
                            Mus musculus strain CBA/J:0.0004
                          ):0.00014,
                          Mus musculus strain DBA/2J:0.00026
                        ):0.0001,
                        Mus musculus strain A/J:0.00036
                      ):2e-05,
                      (
                        Mus musculus strain BALB/cJ:0.00017,
                        Mus musculus strain NOD/ShiLtJ:0.00048
                      ):0.00015
                    ):6e-05,
                    Mus musculus strain AKR/J:0.0003
                  ):0.00011,
                  Mus musculus strain FVB/NJ:0.00148
                ):8e-05,
                (
                  (
                    (
                      Mus musculus reference CL57BL6 strain:5e-05,
                      Mus musculus strain C57BL/6NJ:0.00035
                    ):0.00041,
                    Mus musculus strain NZO/HlLtJ:0.00036
                  ):0.00019,
                  Mus musculus domesticus strain WSB/EiJ:0.00097
                ):0.00021
              ):0.00012,
              (
                Mus musculus strain 129S1/SvImJ:0.00014,
                Mus musculus strain LP/J:0.00029
              ):0.00019
            ):0.00152,
            Mus musculus castaneus strain CAST/EiJ:0.00115
          ):0.00029,
          Mus musculus musculus strain PWK/PhJ:0.0019
        ):0.00159,
        Mus spretus reference strain:0.00345
      ):0.0006,
      Mus spicilegus:0.00363
    ):0.00316,
    Mus caroli strain CAROLI_EIJ:0.00867
  ):0.00509,
  Mus pahari strain PAHARI_EIJ:0.01121
):0.00907,
Rattus norvegicus reference strain:0.02018
);


First, Enredo is used to build a set of co-linear regions between the genomes. Then Pecan aligns
these whole set of sequences. Last, Ortheus uses the Pecan alignments to infer the ancestral
sequences.

Enredo is a graph-based method. The initial graph is built from a mapping of a set of anchors on
every genome. Note that each anchor can map several times on a single genome. Enredo uses this
information to define co-linear regions. Read more about Enredo: https://github.com/jherrero/enredo

Pecan is a global multiple sequence alignment program that makes practical the probabilistic
consistency methodology for significant numbers of sequences of practically arbitrary length. As
input it takes a set of sequences and a phylogenetic tree. The parameters and heuristics it employs
are highly user configurable, it is written entirely in Java and also requires the installation of
Exonerate. Read more about Pecan: https://github.com/benedictpaten/pecan

Ortheus is a probabilistic method for the inference of ancestor (a.k.a tree) alignments. The main
contribution of Ortheus is the use of a phylogenetic model incorporating gaps to infer insertion
and deletion events. Read more about Ortheus: https://github.com/benedictpaten/ortheus

Alignments are grouped by mouse chromosome, and then by coordinate system. Alignments containing
duplications in mouse are dumped once per duplicated segment. The files named *.other*.emf contain
alignments that do not include any mouse region. Each file contains up to 200 alignments.

An emf2maf parser is available with the ensembl compara API, in the scripts/dumps directory.
Alternatively you can download it using the GitHub frontend:
https://github.com/Ensembl/ensembl-compara/raw/master/scripts/dumps/emf2maf.pl