This directory contains all the 60-way Pecan 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 was:
 - Opossum (ASM229v1)
 - Elephant (loxAfr3)
 - Greater horseshoe bat (mRhiFer1_v1.p)
 - Narwhal (NGI_Narwhal_1)
 - Beluga whale (ASM228892v3)
 - Vaquita (mPhoSin1.pri)
 - Sperm whale (ASM283717v2)
 - Blue whale (mBalMus1.v2)
 - Yarkand deer (CEY_v1)
 - Goat (ARS1)
 - Hybrid - Bos Indicus (UOA_Brahman_1)
 - Domestic yak (LU_Bosgru_v3.0)
 - Pig (Sscrofa11.1)
 - Chacoan peccary (CatWag_v2_BIUU_UCD)
 - Arabian camel (CamDro2)
 - Horse (EquCab3.0)
 - Lion (PanLeo1.0)
 - Leopard (PanPar1.0)
 - Dingo (ASM325472v1)
 - Dog (ROS_Cfam_1.0)
 - Mouse Lemur (Mmur_3.0)
 - Gibbon (Nleu_3.0)
 - Sumatran orangutan (Susie_PABv2)
 - Gorilla (gorGor4)
 - Human (GRCh38)
 - Bonobo (panpan1.1)
 - Chimpanzee (Pan_tro_3.0)
 - Vervet-AGM (ChlSab1.1)
 - Crab-eating macaque (Macaca_fascicularis_6.0)
 - Macaque (Mmul_10)
 - Olive baboon (Panubis1.0)
 - White-tufted-ear marmoset (mCalJac1.pat.X)
 - Rabbit (OryCun2.0)
 - Guinea Pig (Cavpor3.0)
 - Ryukyu mouse (CAROLI_EIJ_v1.1)
 - Mouse (GRCm39)
 - Shrew mouse (PAHARI_EIJ_v1.1)
 - Prairie vole (MicOch1.0)
 - Chinese hamster CHOK1GS (CHOK1GS_HDv1)
 - Northern American deer mouse (HU_Pman_2.1)
 - Eurasian red squirrel (mSciVul1.1)
 - Alpine marmot (marMar2.1)
 - Platypus (mOrnAna1.p.v1)
 - Eastern brown snake (EBS10Xv2-PRI)
 - Indian cobra (Nana_v5)
 - Green anole (AnoCar2.0v2)
 - Common wall lizard (PodMur_1.0)
 - Argentine black and white tegu (HLtupMer3)
 - Australian saltwater crocodile (CroPor_comp1)
 - Great Tit (Parus_major1.1)
 - Common canary (SCA1)
 - Zebra finch (bTaeGut1_v1.p)
 - Kakapo (bStrHab1_v1.p)
 - Golden eagle (bAquChr1.2)
 - Duck (CAU_duck1.0)
 - Turkey (Turkey_5.1)
 - Chicken (bGalGal1.mat.broiler.GRCg7b)
 - Japanese quail (Coturnix_japonica_2.0)
 - Goodes thornscrub tortoise (rGopEvg1_v1.p)
 - Three-toed box turtle (T_m_triunguis-2.0)

The species tree was:
(
(
  (
    (
      (
        (
          (
            (
              (
                Serinus canaria:0.01609,
                Taeniopygia guttata:0.01971
              ):0.00742,
              Parus major:0.016
            ):0.03999,
            Strigops habroptila:0.03123
          ):0.00363,
          Aquila chrysaetos chrysaetos:0.01652
        ):0.01124,
        (
          (
            (
              Gallus gallus reference breed:0.01082,
              Coturnix japonica:0.0192
            ):0.00137,
            Meleagris gallopavo reference strain:0.01634
          ):0.0295,
          Anas platyrhynchos platyrhynchos:0.03392
        ):0.01143
      ):0.05538,
      Crocodylus porosus:0.06448
    ):0.01298,
    (
      Terrapene triunguis:0.00976,
      Gopherus evgoodei:0.01864
    ):0.04262
  ):0.01135,
  (
    (
      Podarcis muralis:0.05632,
      Salvator merianae:0.0704
    ):0.00787,
    (
      (
        Pseudonaja textilis:0.01587,
        Naja naja:0.01943
      ):0.09114,
      Anolis carolinensis reference strain:0.07557
    ):0.01305
  ):0.07357
):0.02923,
(
  (
    (
      (
        (
          (
            (
              (
                (
                  (
                    (
                      Cricetulus griseus:0.02331,
                      Microtus ochrogaster:0.02605
                    ):0.00176,
                    Peromyscus maniculatus bairdii:0.02125
                  ):0.00606,
                  (
                    (
                      Mus musculus reference CL57BL6 strain:0.00814,
                      Mus caroli strain CAROLI_EIJ:0.00867
                    ):0.00509,
                    Mus pahari strain PAHARI_EIJ:0.01121
                  ):0.02408
                ):0.03858,
                Cavia porcellus:0.06846
              ):0.00199,
              (
                Marmota marmota marmota:0.02069,
                Sciurus vulgaris:0.02098
              ):0.01752
            ):0.0053,
            Oryctolagus cuniculus:0.05566
          ):0.00284,
          (
            (
              (
                (
                  (
                    (
                      (
                        (
                          Pan troglodytes:0.00168,
                          Pan paniscus:0.00306
                        ):0.00278,
                        Homo sapiens:0.00274
                      ):0.00104,
                      Gorilla gorilla gorilla:0.00701
                    ):0.00342,
                    Pongo abelii:0.00671
                  ):0.00117,
                  Nomascus leucogenys:0.01685
                ):0.00357,
                (
                  (
                    (
                      Macaca mulatta:0.00115,
                      Macaca fascicularis:0.00533
                    ):0.0028,
                    Papio anubis:0.00472
                  ):0.00117,
                  Chlorocebus sabaeus:0.00518
                ):0.00859
              ):0.00562,
              Callithrix jacchus:0.02358
            ):0.01713,
            Microcebus murinus:0.03684
          ):0.00432
        ):0.00439,
        (
          (
            (
              (
                (
                  (
                    (
                      (
                        (
                          Monodon monoceros:0.00197,
                          Delphinapterus leucas:0.00236
                        ):0.00247,
                        Phocoena sinus:0.0061
                      ):0.00841,
                      Physeter catodon:0.01179
                    ):0.00166,
                    Balaenoptera musculus:0.01245
                  ):0.01498,
                  (
                    (
                      (
                        Bos indicus x Bos taurus:0.00251,
                        Bos grunniens:0.01194
                      ):0.01023,
                      Capra hircus reference breed:0.01093
                    ):0.00393,
                    Cervus hanglu yarkandensis:0.0123
                  ):0.02052
                ):0.00458,
                (
                  Catagonus wagneri:0.01739,
                  Sus scrofa reference breed:0.02226
                ):0.01581
              ):0.00238,
              Camelus dromedarius:0.03147
            ):0.00795,
            Rhinolophus ferrumequinum:0.0438
          ):0.00124,
          (
            (
              (
                Panthera pardus:0.00079,
                Panthera leo:0.00164
              ):0.02393,
              (
                Canis lupus familiaris reference breed:0.00154,
                Canis lupus dingo:0.00155
              ):0.0263
            ):0.01067,
            Equus caballus breed thoroughbred:0.02949
          ):0.00143
        ):0.00618
      ):0.005,
      Loxodonta africana:0.05129
    ):0.05693,
    Monodelphis domestica:0.08729
  ):0.02069,
  Ornithorhynchus anatinus:0.11151
):0.04523
);


First, Mercator is used to build a synteny map between the genomes and then Pecan builds alignments
in these syntenic regions.

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

GERP scores the conservation of each position in the alignment and defines constrained elements
based on these conservation scores. Read more about Gerp:
http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html

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