5 1008 ACXM GAG GGG GAA GAG GCG GTC AAC GAG AAG CAG CCA CAG TAC AGC TGG GAC CAG CGG GCC AAG ATT GAT CCT AAA GAC TAC ATG TTT TCT GGA CTG AAG GAT GAA ACA GTT GGA CGT TTA CCT GGG AAA GTT GCA GGC CAA CAG TTT GTT ATT CAG GAC TGT GAA AAC TGC AAT ATT TAC ATC TTT GAC CAT TCG GCT ACA ATT ACT ATT GAT GAC TGC ACA GGC TGC CGA ATC TTT TTG GGA CCT GTC AAA GGC AGC GTG TTT TTC CGT GAC TGC AAG GAT TGC AAA TGT GTA GTG GCT TGT CAA CAG TTT CGC ACT CGA GAC TGC AGA AAG ATG GAA GTG TTT CTG TGC TGT GCC ACC CAA CCC ATT ATC GAA TCA TCT ACG GGT ATG AAG TTT GGG TGC TTC CAG TAC TAC TAT CCA GAA TTG GCT TTG CAG ATG AAG GAC GCA GGG CTG AGC ATC TTT AAC AAT ACA TGG AGC AAT ATC CAT GAC TTC ACA CCT GTC TCA GGA GAG AAC AAC TGG GGT CTT CTA CCA GAA GAT GTC TCT GTT CAA GAG TGT GTA CCA TTG CCA ACT ATT GAA GAA TTG AAG GGT GTC AGG ATC TCA ACT GAT GGC AAC AGA AGC ATT ATT CCG GTG ACA CAA GGG AGA CGT CAG AAA CAC AGC GAG GAG TCC TGC CTT GTG GTA TTC TTT GCT GGG GAT TAT ACC ACT GCC AAT GCG AGG AAG TTG ATT GAT GAG ATG ACT GGC AAA AAT TTT GGG CTA GTG CAT ACT AAA GAA GTT CCA ATG AAA GCG GAT GAT GCT CAT CGT GTT TTC CAG CAA AGA GCG CCT GAA TTT CTC CCT TTA CTT GAA AAA GGT CCT GTT GTT GCT CTG GAG TTC AAT GGA GAT GGC ACG ATA GCA GCC TGC CAA GAA ATT GTT GCA AAT GTC TTC AGT GGA GCT AAG GTT TTT GTA TCT GAG GAC AAA TTA TCT GCT TCC AGG GAA GTA GAC AAC TTC TAT AAC TTT GCT GAT ATG CAG ATG GGA ATG SM8_m GAG GGC GAG GAG AAG GAG AAG CAG CTG CAG CCG CAG TAC AGT TGG GAC CAG AGA GCC AAG ATT GAT CCC AAA GAT TAC ATG TTT TCT GGA CTC AAG GAT GAA ACA GTA GGA CGT TTA CCT GGG AAA GTT GCA GGT CAA CAA TTT GTT ATT CAG GAC TGT GAA AAC TGC AAT ATC TAC ATT TTT GAC CAT TCT GCT ACA ATT ACC ATC GAT GAC TGT ACA GGT TGC CGA ATC TTT TTG GGA CCT GTC AAA GGT AGT GTG TTT TTT CGT GAT TGC AAA GAT TGT AAA TGT GTA GTG GCT TGT CAA CAG TTT CGT ACC CGG GAC TGC AGA AAG ATG GAA GTG TTT CTG TGC TGT GCC ACC CAA CCC ATT ATT GAA TCA TCT ACG GGT ATG AAG TTT GGG TGT TTC CAG TAC TAT TAT CCA GAG CTG GCT TTT CAG ATG AAA GAT GCT GGG CTG AGC ATC TTT AAC AAC ACT TGG AGC AAT ATC CAT GAC TTC ACA CCA GTC TCG GGG GAG AAC AAC TGG AGT CTT TTA GCT GAA GAT GCC TCA GTT CAG GAT TAT GTA CCA TTG CCA GCT GTT GAA GAA TTG AAA GCT GTC AGG ATC TCA ACT GAT ACC AAC CGG AGC ATT ATT CCA GTA ACA CAG GGG CGG CAT CAC AAA CAC AGT GAG GAG TCC TGC CTT GCA ATA TTC TTT GCT GGG GAT TAT ACA ACT GCC AAT GCT AGA AAG TTA ATT GAT GAG ATG ACT GGC AAA GGC TTT TGG CTG GTG CAG ACC AAA GAA GTT CCA ATG AAA TCT GAT GAT GCT CAT CGA GTG TTC CAG CAA AGA GCA TCT GAA TTC ATC CCT TTA CTT GAA AAA GGT CCT GTT GTT GCT CTA GAG TTC AAT GGA GAT GGT TCT GTA GCA GCC TGT CAA GAT ATT GTT ACC AGT GTC TTC AGT GGA GCT AAA GTT TTT GTA TCT GAG GAC AAG TCA TCT GCT TCA AGA GAA GTA GAC AAC TTT TAT AAC TTT GCT GAT ATG CAG ATG GGA ATG Hmaculata GAG AAG GCT ACT CCT GAG AAG CAG CAG CAA CCG CAG TAC AGT TGG GAC CAG AGA GCC AAG ATT GAT CCC AAA GAT TAC ATG TTT TCT GGA CTC AAG GAT GAA ACC GTA GGA CGT TTA CCT GGG AAA GTT GCA GGT CAA CAG TTT GTT ATT CAG GAC TGT GAA AAC TGC AAT ATC TAC ATT TTT GAC CAT TCT GCT ACA ATT ACT ATC GAT GAC TGC ACA GGT TGC CGA ATC TTT TTG GGA CCT GTC AAA GGT AGT GTG TTT TTT CGT GAT TGC AAA GAA TGT AAA TGC GTA GTG GCT TGT CAA CAG TTT CGT ACC CGG GAC TGC AGA AAG ATG GAA GTG TTT TTG TGC TGT GCC ACT CAA CCC ATT ATT GAA TCA TCT ACG GGT CTG AAG TTT GGG TGT TTC CAG TAC TAT TAT CCA GAA CTG GCT TTT CAG ATG AAA GAT GCT GGG CTG AGC ATC TTT AAC AAC ACA TGG AGC AAT ATC CAT GAC TTC ACA CCA GTC TCG GGG GAG AAC AAC TGG AGT CTT TTA GCT GAA GAT GCC TCA GTT CAG GAT TAT GTA CCA TTG CCA GCT GTT GAA GAA TTG AAA ACT GTC AGG ATC TCA ACT GAT ACC AAC AGA AGC ATT ATT CCA GTA ACA CGT GGG CGA CGT CAG AAA CAT AGT GAG GAG TCC TGC CTT GCC GTA TTC TTC GCA GGG GAT TAT ACA ACT GCC AAT GCT AGG AAG TTA ATT GAT GAG ATG ACT GGC AAA GGC TTT TGG TTG GTG CAA ACC AAA GAA GTT CCA ATG AAA GCT GAC GAT GCT CAT CGA GTG TTC CAG CAA AGA GCA TCT GAA TTT ATC CCT TTA CTT GAA AAA GGT CCT GTT GTT GCT CTA GAA TTC AAT GGA GAT GGT TCT GTA GCA GCC TGT CAA GAT ATT GTT AAC AGC ATC TTC AGT GGA GCT AAA GTT TTT GTA TCT GAG GAC AAA TCA TCT GCT TCA AGA GAA GTA GAC AAC TTC TAT AAC TTT GCT GAT ATG CAG ATG GGA ATG NHlacerata GAG AAG GCC ACT CCT GAG AAG CAA CAG CAA CCG CAG TAC AGT TGG GAC CAG AGA GCC AAG ATT GAT CCC AAA GAT TAC ATG TTT TCT GGA CTC AAG GAT GAA ACA GTA GGA CGT TTA CCT GGG AAA GTT GCA GGT CAA CAG TTT GTT ATT CAG GAC TGT GAA AAC TGC AAT ATC TAC ATT TTT GAC CAT TCT GCT ACA ATT ACT ATT GAT GAC TGC ACA GGT TGC CGA ATC TTT TTG GGA CCT GTC AAA GGT AGT GTG TTT TTT CGT GAT TGC AAA GAT TGT AAA TGC GTA GTG GCT TGT CAA CAG TTT CGT ACC CGG GAC TGC AGA AAG ATG GAA GTG TTT CTG TGC TGT GCC ACC CAA CCC ATT ATT GAA TCA TCT ACG GGT CTG AAG TTT GGG TGT TTC CAG TAC TAT TAT CCA GAA CTG GCT TTT CAG ATG AAG GAT GCT GGG CTG AGC ATC TTT AAC AAT ACA TGG AGC AAT ATC CAT GAC TTC ACA CCA GTC TCA GGG GAG AAC AAC TGG AGT CTT TTA GCT GAA GAT GCC TCA GTT CAG GAT TAT GTA CCA TTG CCA GCT GTT GAA GAA TTG AAA GCT GTC AGG ATC TCA ACT GAT ACC AAC AGA AGC ATT ATT CCA GTA ACA CGT GGG CGA CGT CAG AAA CAT AGT GAG GAG TCC TGC CTT GCC GTA TTC TTC GCT GGG GAT TAT ACA ACT GCC AAT GCT AGG AAG TTA ATT GAT GAG ATG ACT GGC AAA GGC TTT TGG TTG GTG CAA ACC AAA GAA GTT CCA ATG AAA GCC GAC GAT GCT CAC CGA GTG TTC CAG CAA AGA GCA TCT GAA TTT ATC CCT TTA CTT GAA AAA GGT CCT GTT GTT GCT CTA GAA TTC AAT GGA GAT GGT TCT GTA GCA GCC TGT CAA GAT ATC GTT AAC AGC GTC TTC AGT GGA GCT AAA GTT TTT GTA TCT GAG GAC AAG TCA TCT GCT TCA AGA GAA GTA GAC AAC TTC TAT AAC TTT GCT GAT ATG CAG ATG GGA ATG SHlacerata GAG AAG GCC ACT CCT GAG AAG CAG CAG CAA CCG CAG TAC AGT TGG GAC CAG AGA GCC AAG ATT GAT CCC AAA GAT TAC ATG TTT TCT GGA CTC AAG GAT GAA ACA GTA GGA CGT TTA CCT GGG AAA GTT GCA GGT CAA CAG TTT GTT ATT CAG GAC TGT GAA AAC TGC AAT ATC TAC ATT TTT GAC CAT TCT GCT ACA ATT ACT ATT GAT GAC TGC ACA GGT TGC CGA ATC TTT TTG GGA CCT GTC AAA GGT AGT GTG TTT TTT CGT GAT TGC AAA GAT TGT AAA TGC GTA GTG GCT TGT CAA CAG TTT CGT ACC CGG GAC TGC AGA AAG ATG GAA GTG TTT CTG TGC TGT GCC ACC CAA CCC ATT ATT GAA TCA TCT ACG GGT CTG AAG TTT GGG TGT TTC CAG TAC TAT TAT CCA GAA CTG GCT TTT CAG ATG AAG GAT GCT GGG CTG AGC ATC TTT AAC AAT ACA TGG AGC AAT ATC CAT GAC TTC ACA CCA GTC TCA GGG GAG AAC AAC TGG AGT CTT TTA GCT GAA GAT GCC TCA GTT CAG GAT TAT GTA CCA TTG CCA GCT GTT GAA GAA TTG AAA ACT GTC AGG ATC TCA ACT GAT ACC AAC AGA AGC ATT ATT CCA GTA ACA CGT GGG CGA CGT CAG AAA CAT AGT GAG GAG TCC TGC CTT GCC GTA TTC TTC GCT GGG GAT TAT ACA ACT GCC AAT GCT AGG AAG TTA ATT GAT GAG ATG ACT GGC AAA GGC TTT TGG TTG GTG CAA ACC AAA GAA GTT CCA ATG AAA GCC GAC GAT GCT CAC CGA GTG TTC CAG CAA AGA GCA TCT GAA TTT ATC CCT TTA CTT GAA AAA GGT CCT GTT GTT GCT CTA GAA TTC AAT GGA GAT GGT TCT GTA GCA GCC TGT CAA GAT ATC GTT AAC AGC GTC TTC AGT GGA GCT AAA GTT TTT GTA TCT GAG GAC AAG TCA TCT GCT TCA AGA GAA GTA GAC AAC TTC TAT AAC TTT GCT GAT ATG CAG ATG GGA ATG Printing out site pattern counts 5 459 P ACXM AAA AAA AAC AAC AAG AAG AAG AAG AAT AAT AAT AAT ACA ACA ACA ACC ACC ACG ACG ACT ACT ACT ACT AGA AGA AGA AGC AGC AGG AGG AGG AGT ATA ATC ATC ATG ATG ATT ATT ATT ATT ATT CAA CAA CAA CAC CAG CAG CAG CAG CAT CAT CAT CCA CCA CCA CCC CCG CCT CCT CCT CCT CGA CGA CGC CGG CGT CGT CGT CTA CTA CTC CTG CTG CTG CTG CTT GAA GAA GAA GAA GAC GAC GAG GAG GAG GAG GAG GAT GAT GAT GCA GCA GCA GCC GCG GCG GCG GCG GCT GCT GGA GGA GGC GGC GGC GGG GGG GGG GGT GGT GGT GTA GTA GTC GTC GTC GTC GTG GTG GTG GTT GTT GTT TAC TAC TAT TCA TCA TCC TCC TCG TCT TCT TGC TGC TGC TGG TGT TGT TGT TTA TTA TTC TTC TTC TTG TTG TTG TTG TTT TTT TTT SM8_m ... ..G ... ..G ..A ..A ... CT. ..C ... .G. GGC ... ... ..T ..A ... ... T.T ..C ..C ... G.. ... C.G C.G ... ..T ..A ..A ... ... G.. ... ..T ... ... ..C ..C ... ... G.. ... ..G ..G ... ..A ..C ... ... ..G ... ... ... ..G G.T ... ..A ..A ..C ... T.. ... ..G ..T A.A .A. ..A ... ..G T.. A.. ..A ..C ... ... ... ... ..G ..G ..T ... ..T C.. ... ... ... ..T ... ... ... A.C ... ..T ... AA. ..A ..T T.T ... ... ... ..G AC. ... ..T ..C ... T.. A.. .C. ... A.. ... .AG .C. ... ... .CA ..A ... ..A ..G ... ... ..T ... ... ..G ..A ... ..T ..A ... ... ..T ..T ... .A. ... ... .C. ... ... ..T ..T C.. ..A ... ..T ..C ... ... Hmaculata ... ... ... ..G ..A ..A ... C.. ..C ... .GC GGC ... ..C ... ..A ..T ... T.T ..C ... ... G.. ... ... C.. ... ..T ..A ... ... ... G.. ... ..T ... C.. ..C ..C ... ... G.. ... ..G .GT ..T ... ... ..A ... ..A ... ... ... ..G G.T ... ..A ..A ..C ... T.. ... ..G ..T A.A ... ..A ... T.G T.. A.. ..A ..C ... T.. ... ... ... .CT ..T ... ..T C.. ACT ..A ... ..T ..A ..C ... AAC ... ..T ... C.T ..A ..T ..T ..A ... ... ..G AC. ... ..T AA. ... T.. A.. AC. ... ... ... .AG .C. A.. ... .CC ..A ... ..A ..G ... ... ..T ... ... ..G ..A ... ..T ..A ... ... ... ..T ... .A. ..C ... .C. ... ... ... ..T C.. ..A ... ..T ... ..C ... NHlacerata ... ..G ... ..G ..A ... ... C.. ... ... .GC GGC ... ... ... ..A ... ... T.T ..C ... ... G.. ... ... C.. ... ..T ..A ... ... ... G.. ... ..T ... C.. ..C ... ..C ... G.. ... ..G .GT ..T ... ... ..A ... ..A ..C ... ... ..G G.T ... ..A ..A ..C ... T.. ... ..G ..T A.A ... ..A ... T.G T.. A.. ..A ..C ... ... ... ... ... .CC ..T ... ..T C.A ACT ..A ... ..T ... ..C ... AAC ... ..T ... C.T ..A ..T ..C ... ... ... ..G AC. ... ..T AA. ... T.. A.. .C. ... ... ... .AG .C. ... ... .CC ..A ... ..A ..G ... ... ..T ... ... ... ..A ... ..T ..A ... ... ... ..T ... .A. ..C ... .C. ... ... ... ..T C.. ..A ... ..T ... ..C ... SHlacerata ... ..G ... ..G ..A ... ... C.. ... ... .GC GGC ... ... ... ..A ... ... T.T ..C ... ... G.. ... ... C.. ... ..T ..A ... ... ... G.. ... ..T ... C.. ..C ... ..C ... G.. ... ..G .GT ..T ... ... ..A ... ..A ..C ... ... ..G G.T ... ..A ..A ..C ... T.. ... ..G ..T A.A ... ..A ... T.G T.. A.. ..A ..C ... ... ... ... ... .CC ..T ... ..T C.. ACT ..A ... ..T ... ..C ... AAC ... ..T ... C.T ..A ..T ..C ... ... ... ..G AC. ... ..T AA. ... T.. A.. AC. ... ... ... .AG .C. ... ... .CC ..A ... ..A ..G ... ... ..T ... ... ... ..A ... ..T ..A ... ... ... ..T ... .A. ..C ... .C. ... ... ... ..T C.. ..A ... ..T ... ..C ... 9 1 7 1 3 1 5 1 1 4 1 1 4 1 1 1 1 1 1 2 1 3 1 2 1 1 3 3 1 1 1 1 1 4 2 8 1 1 1 1 7 1 5 1 1 1 1 1 1 8 1 1 2 4 1 1 1 1 1 1 4 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 3 11 1 1 1 8 3 1 1 1 6 1 1 1 10 1 2 1 4 1 1 1 1 1 8 6 1 1 1 4 1 5 1 1 1 2 1 4 1 1 1 3 1 1 4 1 1 8 4 1 3 2 1 1 1 1 1 4 6 1 3 3 1 1 3 1 2 6 1 1 1 1 3 1 1 1 12 CODONML (in paml version 4.9i, September 2018) OG0009663.phy Model: several dN/dS ratios for branches, omega = 1.000 fixed Codon frequency model: F3x4 Site-class models: PositiveSelection ns = 5 ls = 336 Codon usage in sequences ---------------------------------------------------------------------------------------------------------------------- Phe TTT 14 16 15 15 15 | Ser TCT 5 8 7 7 7 | Tyr TAT 3 5 5 5 5 | Cys TGT 5 8 6 6 6 TTC 8 7 8 8 8 | TCC 2 1 1 1 1 | TAC 5 4 4 4 4 | TGC 10 6 8 8 8 Leu TTA 3 4 4 4 4 | TCA 3 5 5 6 6 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 6 3 5 4 4 | TCG 1 1 1 0 0 | TAG 0 0 0 0 0 | Trp TGG 3 4 4 4 4 ---------------------------------------------------------------------------------------------------------------------- Leu CTT 3 3 3 3 3 | Pro CCT 7 4 5 5 5 | His CAT 4 4 4 3 3 | Arg CGT 4 3 5 5 5 CTC 1 1 1 1 1 | CCC 1 2 2 2 2 | CAC 1 2 0 1 1 | CGC 1 0 0 0 0 CTA 2 1 1 1 1 | CCA 6 6 6 6 6 | Gln CAA 7 6 7 8 7 | CGA 2 2 3 3 3 CTG 4 5 3 4 4 | CCG 1 1 1 1 1 | CAG 11 13 13 12 13 | CGG 1 3 1 1 1 ---------------------------------------------------------------------------------------------------------------------- Ile ATT 11 10 10 10 10 | Thr ACT 7 4 7 5 6 | Asn AAT 7 4 4 5 5 | Ser AGT 1 6 5 5 5 ATC 6 7 8 7 7 | ACC 2 6 4 4 4 | AAC 8 8 9 8 8 | AGC 6 3 4 4 4 ATA 1 1 0 0 0 | ACA 6 6 6 7 7 | Lys AAA 10 13 14 12 12 | Arg AGA 4 5 5 5 5 Met ATG 9 9 8 8 8 | ACG 2 1 1 1 1 | AAG 10 8 7 9 9 | AGG 3 1 2 2 2 ---------------------------------------------------------------------------------------------------------------------- Val GTT 10 9 9 9 9 | Ala GCT 9 14 14 14 13 | Asp GAT 12 17 15 16 16 | Gly GGT 4 6 6 6 6 GTC 6 4 3 4 4 | GCC 4 5 6 8 8 | GAC 11 8 9 9 9 | GGC 6 3 2 2 2 GTA 5 7 8 8 8 | GCA 4 4 4 3 3 | Glu GAA 14 11 14 13 13 | GGA 7 6 6 6 6 GTG 6 5 5 5 5 | GCG 4 0 0 0 0 | GAG 10 11 7 7 7 | GGG 7 6 6 6 6 ---------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: ACXM position 1: T:0.20238 C:0.16667 A:0.27679 G:0.35417 position 2: T:0.28274 C:0.19048 A:0.33631 G:0.19048 position 3: T:0.31548 C:0.23214 A:0.22024 G:0.23214 Average T:0.26687 C:0.19643 A:0.27778 G:0.25893 #2: SM8_m position 1: T:0.21429 C:0.16667 A:0.27381 G:0.34524 position 2: T:0.27381 C:0.20238 A:0.33929 G:0.18452 position 3: T:0.36012 C:0.19940 A:0.22917 G:0.21131 Average T:0.28274 C:0.18948 A:0.28075 G:0.24702 #3: Hmaculata position 1: T:0.21726 C:0.16369 A:0.27976 G:0.33929 position 2: T:0.27083 C:0.20833 A:0.33333 G:0.18750 position 3: T:0.35714 C:0.20536 A:0.24702 G:0.19048 Average T:0.28175 C:0.19246 A:0.28671 G:0.23909 #4: NHlacerata position 1: T:0.21429 C:0.16667 A:0.27381 G:0.34524 position 2: T:0.27083 C:0.20833 A:0.33333 G:0.18750 position 3: T:0.35417 C:0.21131 A:0.24405 G:0.19048 Average T:0.27976 C:0.19544 A:0.28373 G:0.24107 #5: SHlacerata position 1: T:0.21429 C:0.16667 A:0.27679 G:0.34226 position 2: T:0.27083 C:0.20833 A:0.33333 G:0.18750 position 3: T:0.35417 C:0.21131 A:0.24107 G:0.19345 Average T:0.27976 C:0.19544 A:0.28373 G:0.24107 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 75 | Ser S TCT 34 | Tyr Y TAT 23 | Cys C TGT 31 TTC 39 | TCC 6 | TAC 21 | TGC 40 Leu L TTA 19 | TCA 25 | *** * TAA 0 | *** * TGA 0 TTG 22 | TCG 3 | TAG 0 | Trp W TGG 19 ------------------------------------------------------------------------------ Leu L CTT 15 | Pro P CCT 26 | His H CAT 18 | Arg R CGT 22 CTC 5 | CCC 9 | CAC 5 | CGC 1 CTA 6 | CCA 30 | Gln Q CAA 35 | CGA 13 CTG 20 | CCG 5 | CAG 62 | CGG 7 ------------------------------------------------------------------------------ Ile I ATT 51 | Thr T ACT 29 | Asn N AAT 25 | Ser S AGT 22 ATC 35 | ACC 20 | AAC 41 | AGC 21 ATA 2 | ACA 32 | Lys K AAA 61 | Arg R AGA 24 Met M ATG 42 | ACG 6 | AAG 43 | AGG 10 ------------------------------------------------------------------------------ Val V GTT 46 | Ala A GCT 64 | Asp D GAT 76 | Gly G GGT 28 GTC 21 | GCC 31 | GAC 46 | GGC 15 GTA 36 | GCA 18 | Glu E GAA 65 | GGA 31 GTG 26 | GCG 4 | GAG 42 | GGG 31 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.21250 C:0.16607 A:0.27619 G:0.34524 position 2: T:0.27381 C:0.20357 A:0.33512 G:0.18750 position 3: T:0.34821 C:0.21190 A:0.23631 G:0.20357 Average T:0.27817 C:0.19385 A:0.28254 G:0.24544 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.02112117 0.01285323 0.01433351 0.01234776 0.01570313 0.00955609 0.01065666 0.00918029 0.02585048 0.01573123 0.00000000 0.00000000 0.01446341 0.00880167 0.00000000 0.00845553 0.01650646 0.01004496 0.01120182 0.00964993 0.01227220 0.00746821 0.00832831 0.00717451 0.02020247 0.01229416 0.01371006 0.01181068 0.01130334 0.00687861 0.00767081 0.00660811 0.02745161 0.01670559 0.01862955 0.01604863 0.02040967 0.01242025 0.01385067 0.01193181 0.03359838 0.02044619 0.02280095 0.01964213 0.01879838 0.01143970 0.01275719 0.01098982 0.03431451 0.02088199 0.02328694 0.02006079 0.02551209 0.01552531 0.01731333 0.01491476 0.04199797 0.02555774 0.02850119 0.02455266 0.02349798 0.01429962 0.01594649 0.01373728 TREE # 1: ((3, (4, 5)), 2, 1); MP score: 137 lnL(ntime: 7 np: 11): -2036.859674 +0.000000 6..7 7..3 7..8 8..4 8..5 6..2 6..1 0.075012 0.026543 0.021772 0.006290 0.000004 0.072493 0.382553 2.436180 0.852957 0.094836 0.039081 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.584667 ((3: 0.026543, (4: 0.006290, 5: 0.000004): 0.021772): 0.075012, 2: 0.072493, 1: 0.382553); ((Hmaculata: 0.026543, (NHlacerata: 0.006290, SHlacerata: 0.000004): 0.021772): 0.075012, SM8_m: 0.072493, ACXM: 0.382553); Detailed output identifying parameters kappa (ts/tv) = 2.43618 MLEs of dN/dS (w) for site classes (K=4) site class 0 1 2a 2b proportion 0.85296 0.09484 0.04698 0.00522 background w 0.03908 1.00000 0.03908 1.00000 foreground w 0.03908 1.00000 1.00000 1.00000 Time used: 0:10