From 97a43241526e51a37aa9480a4c0b739fc4b9d851 Mon Sep 17 00:00:00 2001 From: Irwin Jungreis Date: Wed, 13 Jan 2016 18:46:54 -0500 Subject: [PATCH] Added parameters for 58mammals. Uses same matrices as 29 mammals but tree for the 58 placental mammals subset of hg38.100way.commonNames.nh (two names were changed to remove special characters: Star-nosed_mole -> Star_nosed_mole; David's_myotis -> Davids_myotis). --- PhyloCSF_Parameters/58mammals.nh | 172 ++++++++++++++++++++++++++++ PhyloCSF_Parameters/58mammals_coding.ECM | 72 ++++++++++++ PhyloCSF_Parameters/58mammals_noncoding.ECM | 72 ++++++++++++ 3 files changed, 316 insertions(+) create mode 100644 PhyloCSF_Parameters/58mammals.nh create mode 100644 PhyloCSF_Parameters/58mammals_coding.ECM create mode 100644 PhyloCSF_Parameters/58mammals_noncoding.ECM diff --git a/PhyloCSF_Parameters/58mammals.nh b/PhyloCSF_Parameters/58mammals.nh new file mode 100644 index 0000000..d3e6676 --- /dev/null +++ b/PhyloCSF_Parameters/58mammals.nh @@ -0,0 +1,172 @@ +( + ( + ( + ( + ( + ( + ( + ( + ( + ( + ( + Human:0.00655, + Chimp:0.00684 + ):0.00422, + Gorilla:0.008964 + ):0.009693, + Orangutan:0.01894 + ):0.003471, + Gibbon:0.02227 + ):0.01204, + ( + ( + ( + Rhesus:0.004991, + Crab_eating_macaque:0.004991 + ):0.003, + Baboon:0.008042 + ):0.01061, + Green_monkey:0.027 + ):0.025 + ):0.02183, + ( + Marmoset:0.03, + Squirrel_monkey:0.01035 + ):0.01965 + ):0.07261, + Bushbaby:0.13992 + ):0.013494, + Chinese_tree_shrew:0.174937 + ):0.002, + ( + ( + ( + Squirrel:0.125468, + ( + Lesser_Egyptian_jerboa:0.1, + ( + ( + Prairie_vole:0.08, + ( + Chinese_hamster:0.04, + Golden_hamster:0.04 + ):0.04 + ):0.06, + ( + Mouse:0.084509, + Rat:0.091589 + ):0.047773 + ):0.06015 + ):0.1 + ):0.022992, + ( + Naked_mole_rat:0.1, + ( + Guinea_pig:0.065629, + ( + Chinchilla:0.06, + Brush_tailed_rat:0.1 + ):0.06 + ):0.05 + ):0.06015 + ):0.025746, + ( + Rabbit:0.114227, + Pika:0.201069 + ):0.101463 + ):0.015313 + ):0.020593, + ( + ( + ( + Pig:0.12, + ( + ( + Alpaca:0.047275, + Wild_bactrian_camel:0.04 + ):0.04, + ( + ( + Dolphin:0.034688, + Killer_whale:0.039688 + ):0.03, + ( + Tibetan_antelope:0.1, + ( + Cow:0.1, + ( + Sheep:0.05, + Domestic_goat:0.05 + ):0.05 + ):0.01 + ):0.013592 + ):0.025153 + ):0.020335 + ):0.02, + ( + ( + ( + Horse:0.059397, + White_rhinoceros:0.025 + ):0.05, + ( + Cat:0.098612, + ( + Dog:0.052458, + ( + Ferret:0.05, + ( + Panda:0.02, + ( + Pacific_walrus:0.02, + Weddell_seal:0.02 + ):0.02 + ):0.03 + ):0.03 + ):0.02 + ):0.049845 + ):0.006219, + ( + ( + Black_flying_fox:0.05, + Megabat:0.063399 + ):0.05, + ( + Big_brown_bat:0.02, + ( + Davids_myotis:0.04, + Microbat:0.04254 + ):0.05 + ):0.06 + ):0.033706 + ):0.004508 + ):0.011671, + ( + Hedgehog:0.221785, + ( + Shrew:0.169562, + Star_nosed_mole:0.1 + ):0.1 + ):0.056393 + ):0.021227 + ):0.023664, + ( + ( + ( + ( + ( + Elephant:0.002242, + Cape_elephant_shrew:0.05 + ):0.04699, + Manatee:0.1 + ):0.049697, + ( + Cape_golden_mole:0.03, + Tenrec:0.235936 + ):0.01 + ):0.03, + Aardvark:0.03 + ):0.02, + Armadillo:0.169809 + ):0.006717 +); \ No newline at end of file diff --git a/PhyloCSF_Parameters/58mammals_coding.ECM b/PhyloCSF_Parameters/58mammals_coding.ECM new file mode 100644 index 0000000..f894011 --- /dev/null +++ b/PhyloCSF_Parameters/58mammals_coding.ECM @@ -0,0 +1,72 @@ +0.771493279396 +14.5180982851 0.547433994462 +0.829799770357 31.1892114825 0.7020007509 +1.2357249048 0.0591436724948 0.143021129459 0.0723670336788 +0.0491379655094 1.68015082454 0.0198294354489 0.039540785463 10.4536837099 +0.0705620171551 0.0966709944264 1.69743422922 0.142387839362 91.937054195 27.5243026465 +0.0429527042192 0.105163194816 0.0172649210373 2.25040676661 10.8921310832 29.7216988175 32.0319353336 +7.4338524426 0.17080527673 0.354723692547 0.186750900063 1.57462078709 0.053744234112 0.0267286337571 0.0670392311205 +0.15475952294 7.04751773186 0.133727701692 0.272371840933 0.0995168546074 2.91545126347 0.241247972617 0.30307911252 1.14819950914 +0.523684400979 0.193336177917 7.27785844907 0.248082744588 0.28292064082 0.0737402201706 2.22444630107 0.0911973524823 39.1328554206 1.20406413448 +0.173018086183 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