Mercurial > repos > iuc > pal2nal

annotate test-data/inputs/for_paml/test.codeml.ori @ 0:a2a40f3bfbbd draft default tip

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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:06 +0000
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0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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diff changeset
1 CODONML (in paml 3.14, March 2005) test.codon Model: several dN/dS ratios for branches
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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2 Codon frequencies: F3x4
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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3
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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4 ns = 2 ls = 177
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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5 # site patterns = 105
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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6 2 1 1 1 1 1 1 1 1 1 4 3 2 1 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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7 1 1 4 1 1 2 1 1 1 7 2 3 1 2 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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8 2 1 3 1 1 2 2 8 1 1 1 1 1 1 7
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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9 1 1 1 3 1 4 1 1 4 1 1 3 2 1 6
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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10 1 1 1 2 1 1 1 6 2 1 3 1 1 4 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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11 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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12 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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13
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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14
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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15 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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16 BC070280 CTA AAC TGC ATC GTC GCT GTG TCC CAG AAC ATG GGC ATC GGC AAG AAC GGG GAC CTG CCC CCA CCG CTC AGG AAT GAA TTC CAG AGA ACC ACA ACC TCT TCA GTA GAA GGT AAA CAG CTG GTG ATT ATG GGT AAG ACC TGG TCC ATT CCT GAG CGA CCT TTA GGT AGA GTT CTC AGC GAA CTC CCT CCA CAA GGA GCT CAT TTT CTT TCC AGT CTA GAT GAT GCC CTT ACT CCA GCA GTA ATG CTC TGG ATA GTT GGT TAT GCC GGC CAT CTT GTG AGG CAA GAA ACG ATT TTG CTG CCA TAC GTC CAG GTA GAG
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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17 pseudogene ... ... ... ..T ... AA. .AT ... ... ..G ... ... ... AT. .G. ..T ... ... ... ... ..T .A. ... .AA ... A.. ... ..A ... ... ... C.. ... ... .C. ..G ... ... G.A T.A ..A T.. T.A AT. ... .A. ... ..G ... A.. ... .A. ... ... TA. .T. ... G.. ..T ... TC. ..A ..G ... A.. C.. .C. ... ... GA. ... ..G .G. ... ... .G. .T. .T. ... CA. G.. T.T .TT .C. ..G ..A ... T.. .A. ... T.. ... T.. ..G C.. ... GG. ..A ..C ... ... ..G G.. ... ..A
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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18
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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19 Codon usage in sequences
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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20 --------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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21 Phe TTT 6 10 | Ser TCT 3 3 | Tyr TAT 3 4 | Cys TGT 0 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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22 TTC 3 3 | TCC 3 3 | TAC 2 2 | TGC 1 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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23 Leu TTA 4 7 | TCA 1 1 | *** TAA 0 0 | *** TGA 0 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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24 TTG 1 0 | TCG 0 1 | TAG 0 0 | Trp TGG 2 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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25 --------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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26 Leu CTT 4 2 | Pro CCT 3 5 | His CAT 2 1 | Arg CGT 0 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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27 CTC 5 2 | CCC 1 2 | CAC 0 0 | CGC 0 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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28 CTA 3 3 | CCA 6 3 | Gln CAA 3 6 | CGA 1 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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29 CTG 3 2 | CCG 1 1 | CAG 4 3 | CGG 0 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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30 --------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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31 Ile ATT 5 6 | Thr ACT 1 1 | Asn AAT 7 9 | Ser AGT 3 4
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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32 ATC 3 3 | ACC 3 1 | AAC 3 2 | AGC 1 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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33 ATA 1 1 | ACA 2 3 | Lys AAA 8 11 | Arg AGA 3 3
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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34 Met ATG 6 4 | ACG 1 1 | AAG 9 8 | AGG 2 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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35 --------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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36 Val GTT 4 3 | Ala GCT 2 0 | Asp GAT 5 5 | Gly GGT 5 4
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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37 GTC 2 3 | GCC 2 1 | GAC 4 6 | GGC 5 3
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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38 GTA 3 2 | GCA 1 2 | Glu GAA 11 8 | GGA 1 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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39 GTG 3 4 | GCG 0 0 | GAG 5 7 | GGG 1 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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40 --------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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41
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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42 Codon position x base (3x4) table for each sequence.
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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43
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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44 #1: BC070280
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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45 position 1: T:0.16384 C:0.20339 A:0.32768 G:0.30508
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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46 position 2: T:0.31638 C:0.16949 A:0.37288 G:0.14124
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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47 position 3: T:0.29944 C:0.21469 A:0.27119 G:0.21469
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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48
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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49 #2: pseudogene
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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50 position 1: T:0.20904 C:0.17514 A:0.33333 G:0.28249
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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51 position 2: T:0.31073 C:0.15819 A:0.40678 G:0.12429
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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52 position 3: T:0.32768 C:0.18079 A:0.28814 G:0.20339
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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53
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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54 Sums of codon usage counts
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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55 ------------------------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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56 Phe F TTT 16 | Ser S TCT 6 | Tyr Y TAT 7 | Cys C TGT 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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57 TTC 6 | TCC 6 | TAC 4 | TGC 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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58 Leu L TTA 11 | TCA 2 | *** * TAA 0 | *** * TGA 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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59 TTG 1 | TCG 1 | TAG 0 | Trp W TGG 4
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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60 ------------------------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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61 Leu L CTT 6 | Pro P CCT 8 | His H CAT 3 | Arg R CGT 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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62 CTC 7 | CCC 3 | CAC 0 | CGC 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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63 CTA 6 | CCA 9 | Gln Q CAA 9 | CGA 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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64 CTG 5 | CCG 2 | CAG 7 | CGG 0
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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65 ------------------------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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66 Ile I ATT 11 | Thr T ACT 2 | Asn N AAT 16 | Ser S AGT 7
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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67 ATC 6 | ACC 4 | AAC 5 | AGC 1
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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68 ATA 2 | ACA 5 | Lys K AAA 19 | Arg R AGA 6
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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69 Met M ATG 10 | ACG 2 | AAG 17 | AGG 4
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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70 ------------------------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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71 Val V GTT 7 | Ala A GCT 2 | Asp D GAT 10 | Gly G GGT 9
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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72 GTC 5 | GCC 3 | GAC 10 | GGC 8
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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73 GTA 5 | GCA 3 | Glu E GAA 19 | GGA 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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74 GTG 7 | GCG 0 | GAG 12 | GGG 2
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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75 ------------------------------------------------------------------------------
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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76
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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77
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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78 Codon position x base (3x4) table, overall
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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79
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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80 position 1: T:0.18644 C:0.18927 A:0.33051 G:0.29379
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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81 position 2: T:0.31356 C:0.16384 A:0.38983 G:0.13277
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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82 position 3: T:0.31356 C:0.19774 A:0.27966 G:0.20904
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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83
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84
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85 Nei & Gojobori 1986. dN/dS (dN, dS)
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86 (Note: This matrix is not used in later m.l. analysis.
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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87 Use runmode = -2 for ML pairwise comparison.)
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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88
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89 BC070280
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90 pseudogene 0.5224 (0.1421 0.2721)
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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91
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92 pairwise comparison, codon frequencies: F3x4.
a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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93
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94
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95 2 (pseudogene) ... 1 (BC070280)
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96 lnL =-1014.258355
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97 0.52723 1.94064 0.59797
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98
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99 t= 0.5272 S= 129.6 N= 401.4 dN/dS= 0.5980 dN= 0.1510 dS= 0.2525
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100
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101
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102