source: trunk/GDE/PHYML20130708/phyml/doc/phyml-manual.idx

Last change on this file was 10307, checked in by aboeckma, 11 years ago

added most recent version of phyml
File size: 5.9 KB
Line 
1\indexentry{RAxML|hyperpage}{5}
2\indexentry{GARLI|hyperpage}{5}
3\indexentry{bug|hyperpage}{5}
4\indexentry{compilation|hyperpage}{5}
5\indexentry{MPI|hyperpage}{6}
6\indexentry{bootstrap!parallel|hyperpage}{6}
7\indexentry{run ID|hyperpage}{8}
8\indexentry{$\kappa$|hyperpage}{10}
9\indexentry{ts/tv ratio|hyperpage}{10}
10\indexentry{PAML|hyperpage}{10}
11\indexentry{PHYLIP|hyperpage}{10}
12\indexentry{invariable sites|hyperpage}{10}
13\indexentry{proportion of invariants|hyperpage}{10}
14\indexentry{gamma distribution (discrete)!mean vs. median|hyperpage}{10}
15\indexentry{gamma distribution (discrete)!number of categories|hyperpage}{10}
16\indexentry{gamma distribution (discrete)!shape parameter|hyperpage}{10}
17\indexentry{BioNJ|hyperpage}{12}
18\indexentry{command-line options!\x{--input}|hyperpage}{13}
19\indexentry{command-line options!\x{--data\_type}|hyperpage}{13}
20\indexentry{sequence format!interleaved|hyperpage}{13}
21\indexentry{sequence format!sequential|hyperpage}{13}
22\indexentry{command-line options!\x{--sequential}|hyperpage}{13}
23\indexentry{multiple data sets|hyperpage}{14}
24\indexentry{command-line options!\x{--multiple}|hyperpage}{14}
25\indexentry{command-line options!\x{--pars}|hyperpage}{14}
26\indexentry{bootstrap|hyperpage}{14}
27\indexentry{command-line options!\x{--bootstrap}|hyperpage}{14}
28\indexentry{substitution models!DNA|hyperpage}{14}
29\indexentry{substitution models!amino acids|hyperpage}{14}
30\indexentry{command-line options!\x{--model}|hyperpage}{14}
31\indexentry{custom models|hyperpage}{15}
32\indexentry{command-line options!\x{--aa\_rate\_file}|hyperpage}{15}
33\indexentry{frequencies!nucleotide|hyperpage}{15}
34\indexentry{frequencies!amino-acid|hyperpage}{15}
35\indexentry{stationary frequencies|hyperpage}{15}
36\indexentry{command-line options!\x{-f}|hyperpage}{15}
37\indexentry{$\kappa$|hyperpage}{16}
38\indexentry{ts/tv ratio|hyperpage}{16}
39\indexentry{command-line options!\x{--ts/tv}|hyperpage}{16}
40\indexentry{proportion of invariants|hyperpage}{16}
41\indexentry{invariable sites|hyperpage}{16}
42\indexentry{command-line options!\x{--pinv}|hyperpage}{16}
43\indexentry{gamma distribution (discrete)!number of categories|hyperpage}{16}
44\indexentry{command-line options!\x{--nclasses}|hyperpage}{16}
45\indexentry{gamma distribution (discrete)!shape parameter|hyperpage}{16}
46\indexentry{command-line options!\x{--alpha}|hyperpage}{16}
47\indexentry{gamma distribution (discrete)!mean vs. median|hyperpage}{16}
48\indexentry{command-line options!\x{--use\_median}|hyperpage}{16}
49\indexentry{command-line options!\x{--free\_rates}|hyperpage}{16}
50\indexentry{command-line options!\x{--codpos}|hyperpage}{16}
51\indexentry{NNI|hyperpage}{17}
52\indexentry{SPR|hyperpage}{17}
53\indexentry{command-line options!\x{--search}|hyperpage}{17}
54\indexentry{input tree|hyperpage}{17}
55\indexentry{user tree|hyperpage}{17}
56\indexentry{command-line options!\x{--inputtree}|hyperpage}{17}
57\indexentry{optimisation!topology|hyperpage}{17}
58\indexentry{optimisation!substitution parameters|hyperpage}{17}
59\indexentry{command-line options!\x{-o}|hyperpage}{17}
60\indexentry{random tree|hyperpage}{17}
61\indexentry{command-line options!\x{--rand\_start}|hyperpage}{17}
62\indexentry{command-line options!\x{--n\_rand\_starts}|hyperpage}{17}
63\indexentry{random number|hyperpage}{17}
64\indexentry{command-line options!\x{--r\_seed}|hyperpage}{17}
65\indexentry{likelihood!print site likelihood|hyperpage}{17}
66\indexentry{command-line options!\x{--print\_site\_lk}|hyperpage}{17}
67\indexentry{command-line options!\x{--print\_trace}|hyperpage}{18}
68\indexentry{run ID|hyperpage}{18}
69\indexentry{command-line options!\x{--run\_id}|hyperpage}{18}
70\indexentry{command-line options!\x{--no\_memory\_check}|hyperpage}{18}
71\indexentry{command-line options!\x{--no\_colalias}|hyperpage}{18}
72\indexentry{command-line options!\x{--constrained\_lens}|hyperpage}{18}
73\indexentry{command-line  options!\x{--constraint\_file}|hyperpage}{18}
74\indexentry{command-line options!\x{--quiet}|hyperpage}{18}
75\indexentry{command-line options!\x{--xml}|hyperpage}{19}
76\indexentry{MPI|hyperpage}{19}
77\indexentry{bootstrap!parallel|hyperpage}{19}
78\indexentry{PHYLIP|hyperpage}{20}
79\indexentry{NEXUS|hyperpage}{20}
80\indexentry{sequential|hyperpage}{20}
81\indexentry{interleaved|hyperpage}{20}
82\indexentry{binary characters|hyperpage}{22}
83\indexentry{Newick format|hyperpage}{24}
84\indexentry{multiple data sets|hyperpage}{24}
85\indexentry{PAML|hyperpage}{25}
86\indexentry{XML|hyperpage}{28}
87\indexentry{mixture models|hyperpage}{28}
88\indexentry{partitionned analysis|hyperpage}{29}
89\indexentry{data partitions|hyperpage}{29}
90\indexentry{BEST|hyperpage}{30}
91\indexentry{STEM|hyperpage}{30}
92\indexentry{*BEAST|hyperpage}{30}
93\indexentry{mixture   models|hyperpage}{35}
94\indexentry{partitionned analysis|hyperpage}{35}
95\indexentry{data partitions|hyperpage}{35}
96\indexentry{XML options!{\tt phyml} component|hyperpage}{37}
97\indexentry{XML options!{\tt topology} component|hyperpage}{38}
98\indexentry{XML options!{\tt ratematrices} component|hyperpage}{39}
99\indexentry{XML options!{\tt equfreqs} component|hyperpage}{40}
100\indexentry{XML options!{\tt branchlengths} component|hyperpage}{40}
101\indexentry{XML options!{\tt siterates} component|hyperpage}{41}
102\indexentry{XML options!{\tt partitionelem}   component|hyperpage}{42}
103\indexentry{XML options!{\tt mixtureelem} component|hyperpage}{42}
104\indexentry{lg4x|hyperpage}{44}
105\indexentry{PhyTime|hyperpage}{50}
106\indexentry{serial sample|hyperpage}{52}
107\indexentry{command-line options!\x{--calibration}|hyperpage}{52}
108\indexentry{time scale|hyperpage}{53}
109\indexentry{command-line options!\x{--chain\_len}|hyperpage}{53}
110\indexentry{command-line options!\x{--sample\_freq}|hyperpage}{53}
111\indexentry{command-line options!\x{--fastlk}|hyperpage}{53}
112\indexentry{command-line options!\x{--no\_sequences}|hyperpage}{54}
113\indexentry{command-line options!\x{--rate\_model}|hyperpage}{54}
114\indexentry{Multidivtime|hyperpage}{54}
115\indexentry{BEAST|hyperpage}{54}
116\indexentry{Tracer|hyperpage}{54}
117\indexentry{BEAST|hyperpage}{54}
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