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*.maf contain alignments that do not include any japanese medaka hdrr
region. Each file contains up to 200 alignments.

The MAF format is described at https://genome.ucsc.edu/FAQ/FAQformat.html#format5