Parameters for 100vertebrates (using 29mammal ECMs), 23flies, 49birds

PhyloCSF_Parameters/100vertebrates.nh

@@ -0,0 +1,100 @@
+((((((((((((((((((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):0.234728,
+      (Opossum:0.125686,
+      (Tasmanian_devil:0.1,
+      Wallaby:0.072008):0.05):0.2151):0.071664,
+     Platypus:0.456592):0.109504,
+    (((((Rock_pigeon:0.1,
+        ((Saker_falcon:0.1,
+         Peregrine_falcon:0.1):0.03,
+        (((Collared_flycatcher:0.04,
+          ((White_throated_sparrow:0.034457,
+           Medium_ground_finch:0.041261):0.015,
+          Zebra_finch:0.06):0.01):0.052066,
+         Tibetan_ground_jay:0.06):0.025,
+        (Budgerigar:0.046985,
+        (Puerto_Rican_parrot:0.026,
+        Scarlet_macaw:0.026):0.01):0.04):0.064703):0.06):0.05,
+       (Mallard_duck:0.1,
+       (Chicken:0.041254,
+       Turkey:0.085718):0.031045):0.09):0.22,
+      American_alligator:0.25):0.045143,
+     ((Green_seaturtle:0.1,
+      Painted_turtle:0.1):0.05,
+     (Chinese_softshell_turtle:0.1,
+     Spiny_softshell_turtle:0.1):0.05):0.04):0.01,
+    Lizard:0.447):0.122):0.05,
+   Frog_X._tropicalis:0.977944):0.1,
+  Coelacanth:0.977944):0.111354,
+ (((((((Tetraodon:0.124159,
+       (Fugu:0.103847,
+       Yellowbelly_pufferfish:0.1):0.1):0.09759,
+      (Nile_tilapia:0.1,
+      (Princess_of_Burundi:0.05,
+      (Burtons_mouthbreeder:0.05,
+      (Zebra_mbuna:0.05,
+      Pundamilia_nyererei:0.05):0.05):0.05):0.1):0.1):0.09759,
+     (Medaka:0.38197,
+     Southern_platyfish:0.4):0.1):0.015,
+    Stickleback:0.246413):0.045,
+   Atlantic_cod:0.25):0.22564,
+  (Zebrafish:0.430752,
+  Mexican_tetra:0.4):0.3):0.143632,
+ Spotted_gar:0.4):0.326688):0.2,
+Lamprey:0.975747);

PhyloCSF_Parameters/23flies.nh

@@ -0,0 +1,67 @@
+(
+    (
+        (
+            (
+                (
+                    (
+                        (
+                            (
+                                (
+                                    (
+                                        (
+                                            (
+                                                (
+                                                    dmel:0.0542029,
+                                                    (
+                                                        dsim:0.0213103,
+                                                        dsec:0.0227973
+                                                    ):0.0242621
+                                                ):0.0585014,
+                                                (
+                                                    dyak:0.0889658,
+                                                    dere:0.0771526
+                                                ):0.0254381
+                                            ):0.181996,
+                                            (
+                                                dbia:0.126739,
+                                                dsuz:0.0934222
+                                            ):0.0964756
+                                        ):0.0125386,
+                                        (
+                                            dana:0.132676,
+                                            dbip:0.134892
+                                        ):0.531515
+                                    ):0.00264138,
+                                    deug:0.318569
+                                ):0.0369765,
+                                dele:0.207426
+                            ):0.0025605,
+                            dkik:0.485329
+                        ):0.00243957,
+                        dtak:0.226746
+                    ):0.0143511,
+                    drho:0.195624
+                ):0.0495906,
+                dfic:0.257704
+            ):0.290027,
+            (
+                (
+                    dpse:0.0138526,
+                    dper:0.014979
+                ):0.00969914,
+                dmir:0.0172853
+            ):0.398344
+        ):0.150107,
+        dwil:0.550935
+    ):0.0418275,
+    (
+        (
+            (
+                dvir:0.242786,
+                dmoj:0.321598
+            ):0.090819,
+            dalb:0.436249
+        ):0.0143777,
+        dgri:0.318782
+    ):0.162991
+);