This directory contains all the 32-way Enredo-Pecan-Ortheus (EPO) multiple alignments corresponding
to Release 112 of Ensembl (see http://www.ensembl.org for further details and credits about the
Ensembl project).

The set of species is:
 - Reedfish (fErpCal1.1)
 - Spotted gar (LepOcu1)
 - Tetraodon (TETRAODON8)
 - Fugu (fTakRub1.2)
 - Tongue sole (Cse_v1.0)
 - Channel bull blenny (fCotGob3.1)
 - Lumpfish (fCycLum1.pri)
 - Gilthead seabream (fSpaAur1.1)
 - European seabass (dlabrax2021)
 - Large yellow croaker (L_crocea_2.0)
 - Siamese fighting fish (fBetSpl5.2)
 - Greater amberjack (Sdu_1.0)
 - Turbot (ASM1334776v1)
 - Guppy (Guppy_female_1.0_MT)
 - Platyfish (X_maculatus-5.0-male)
 - Turquoise killifish (Nfu_20140520)
 - Japanese medaka HdrR (ASM223467v1)
 - Indian medaka (Om_v0.7.RACA)
 - Javanese ricefish (OJAV_1.1)
 - Zebra mbuna (M_zebra_UMD2a)
 - Nile tilapia (O_niloticus_UMD_NMBU)
 - Orange clownfish (Nemo_v1)
 - Pinecone soldierfish (fMyrMur1.1)
 - Coho salmon (Okis_V2)
 - Rainbow trout (USDA_OmykA_1.1)
 - Brown trout (fSalTru1.1)
 - Atlantic salmon (Ssal_v3.1)
 - Common carp (Cypcar_WagV4.0)
 - Goldfish (ASM336829v1)
 - Zebrafish (GRCz11)
 - Mexican tetra (Astyanax_mexicanus-2.0)
 - Asian bonytongue (fSclFor1.1)

The species tree was:
(
(
  (
    (
      (
        (
          (
            (
              (
                (
                  (
                    (
                      Seriola dumerili:0.28328,
                      Scophthalmus maximus:0.43711
                    ):0.04712,
                    Betta splendens:0.61838
                  ):0.02713,
                  (
                    (
                      (
                        Dicentrarchus labrax:0.25921,
                        Larimichthys crocea:0.31315
                      ):0.02616,
                      Sparus aurata:0.35136
                    ):0.05336,
                    (
                      Cottoperca gobio:0.40379,
                      Cyclopterus lumpus:0.43779
                    ):0.06945
                  ):0.04663
                ):0.02177,
                Cynoglossus semilaevis:0.78272
              ):0.01598,
              (
                (
                  (
                    Oreochromis niloticus:0.09781,
                    Maylandia zebra:0.15
                  ):0.38407,
                  Amphiprion percula:0.41083
                ):0.03031,
                (
                  (
                    (
                      Xiphophorus maculatus:0.14646,
                      Poecilia reticulata:0.1816
                    ):0.45229,
                    Nothobranchius furzeri:0.61062
                  ):0.0809,
                  (
                    (
                      Oryzias melastigma:0.15829,
                      Oryzias javanicus:0.185
                    ):0.10854,
                    Oryzias latipes:0.28285
                  ):0.47712
                ):0.10514
              ):0.05653
            ):0.04394,
            (
              Takifugu rubripes:0.34799,
              Tetraodon nigroviridis:0.45786
            ):0.4561
          ):0.17596,
          Myripristis murdjan:0.4309
        ):0.34143,
        (
          (
            Salmo salar:0.08069,
            Salmo trutta:0.08624
          ):0.06362,
          (
            Oncorhynchus mykiss:0.09091,
            Oncorhynchus kisutch:0.106
          ):0.07056
        ):0.58607
      ):0.19612,
      (
        (
          (
            Cyprinus carpio carpio:0.15419,
            Carassius auratus:0.20312
          ):0.1699,
          Danio rerio:0.41057
        ):0.4007,
        Astyanax mexicanus:0.76784
      ):0.33377
    ):0.18782,
    Scleropages formosus:0.89574
  ):0.29227,
  Lepisosteus oculatus:0.74728
):0.24864,
Erpetoichthys calabaricus:1.07869
);


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 japanese medaka hdrr chromosome, and then by coordinate system.
Alignments containing duplications in japanese medaka hdrr are dumped once per duplicated segment.
The files named *.other*.emf contain alignments that do not include any japanese medaka hdrr
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