This directory contains all the 44-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:
- Elephant (loxAfr3)
- Mouse Lemur (Mmur_3.0)
- White-tufted-ear marmoset (mCalJac1.pat.X)
- Vervet-AGM (ChlSab1.1)
- Olive baboon (Panubis1.0)
- Macaque (Mmul_10)
- Crab-eating macaque (Macaca_fascicularis_6.0)
- Gibbon (Nleu_3.0)
- Sumatran orangutan (Susie_PABv2)
- Human (GRCh38)
- Bonobo (panpan1.1)
- Chimpanzee (Pan_tro_3.0)
- Gorilla (gorGor4)
- Rabbit (OryCun2.0)
- Alpine marmot (marMar2.1)
- Eurasian red squirrel (mSciVul1.1)
- Guinea Pig (Cavpor3.0)
- Shrew mouse (PAHARI_EIJ_v1.1)
- Ryukyu mouse (CAROLI_EIJ_v1.1)
- Mouse (GRCm39)
- Norway rat - BN/NHsdMcwi (GRCr8)
- Chinese hamster CHOK1GS (CHOK1GS_HDv1)
- Prairie vole (MicOch1.0)
- Northern American deer mouse (HU_Pman_2.1)
- Arabian camel (CamDro2)
- Goat (ARS1)
- Sheep (ARS-UI_Ramb_v2.0)
- Domestic yak (LU_Bosgru_v3.0)
- Cattle (ARS-UCD2.0)
- Hybrid - Bos Indicus (UOA_Brahman_1)
- Yarkand deer (CEY_v1)
- Narwhal (NGI_Narwhal_1)
- Beluga whale (ASM228892v3)
- Vaquita (mPhoSin1.pri)
- Sperm whale (ASM283717v2)
- Blue whale (mBalMus1.v2)
- Chacoan peccary (CatWag_v2_BIUU_UCD)
- Pig (Sscrofa11.1)
- Greater horseshoe bat (mRhiFer1_v1.p)
- Horse (EquCab3.0)
- Dingo (ASM325472v1)
- Dog (ROS_Cfam_1.0)
- Lion (PanLeo1.0)
- Leopard (PanPar1.0)
The species tree was:
(
(
(
(
(
(
(
(
(
Cricetulus griseus CHOK1GS_HDv1:0.02331,
Microtus ochrogaster MicOch1.0:0.02605
):0.00176,
Peromyscus maniculatus bairdii HU_Pman_2.1:0.02125
):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
):0.00907,
Rattus norvegicus reference strain:0.02018
):0.01501
):0.03858,
Cavia porcellus Cavpor3.0:0.06846
):0.00199,
(
Marmota marmota marmota marMar2.1:0.02069,
Sciurus vulgaris mSciVul1.1:0.02098
):0.01752
):0.0053,
Oryctolagus cuniculus OryCun2.0:0.05566
):0.00284,
(
(
(
(
(
(
(
(
Pan troglodytes Pan_tro_3.0:0.00168,
Pan paniscus panpan1.1:0.00306
):0.00278,
Homo sapiens GRCh38:0.00274
):0.00104,
Gorilla gorilla gorilla gorGor4:0.00701
):0.00342,
Pongo abelii Susie_PABv2:0.00671
):0.00117,
Nomascus leucogenys Nleu_3.0:0.01685
):0.00357,
(
(
(
Macaca mulatta Mmul_10:0.00115,
Macaca fascicularis Macaca_fascicularis_6.0:0.00533
):0.0028,
Papio anubis Panubis1.0:0.00472
):0.00117,
Chlorocebus sabaeus ChlSab1.1:0.00518
):0.00859
):0.00562,
Callithrix jacchus mCalJac1.pat.X:0.02358
):0.01713,
Microcebus murinus Mmur_3.0:0.03684
):0.00432
):0.00439,
(
(
(
(
(
(
(
(
(
Monodon monoceros NGI_Narwhal_1:0.00197,
Delphinapterus leucas ASM228892v3:0.00236
):0.00247,
Phocoena sinus mPhoSin1.pri:0.0061
):0.00841,
Physeter catodon ASM283717v2:0.01179
):0.00166,
Balaenoptera musculus mBalMus1.v2:0.01245
):0.01498,
(
(
(
Ovis aries reference breed:0.00323,
Capra hircus reference breed:0.00334
):0.00759,
(
(
Bos taurus reference breed:0.00078,
Bos indicus x Bos taurus UOA_Brahman_1:0.00105
):0.00146,
Bos grunniens LU_Bosgru_v3.0:0.01194
):0.01023
):0.00393,
Cervus hanglu yarkandensis CEY_v1:0.0123
):0.02052
):0.00458,
(
Catagonus wagneri CatWag_v2_BIUU_UCD:0.01739,
Sus scrofa reference breed:0.02226
):0.01581
):0.00238,
Camelus dromedarius CamDro2:0.03147
):0.00795,
Rhinolophus ferrumequinum mRhiFer1_v1.p:0.0438
):0.00124,
(
(
(
Panthera pardus PanPar1.0:0.00079,
Panthera leo PanLeo1.0:0.00164
):0.02393,
(
Canis lupus familiaris reference breed:0.00154,
Canis lupus dingo ASM325472v1:0.00155
):0.0263
):0.01067,
Equus caballus breed thoroughbred:0.02949
):0.00143
):0.00618
):0.005,
Loxodonta africana loxAfr3:0.05129
);
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 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