source: branches/ali/GDE/PHYML20130708/phyml/doc/phyml-manual.out

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

added most recent version of phyml
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1\BOOKMARK [1][-]{section.1}{Availability}{}% 1
2\BOOKMARK [1][-]{section.2}{Authors}{}% 2
3\BOOKMARK [1][-]{section.3}{Overview}{}% 3
4\BOOKMARK [1][-]{section.4}{Bug report}{}% 4
5\BOOKMARK [1][-]{section.5}{Installing PhyML}{}% 5
6\BOOKMARK [2][-]{subsection.5.1}{Sources and compilation}{section.5}% 6
7\BOOKMARK [2][-]{subsection.5.2}{Installing PhyML on UNIX-like systems \(including Mac OS\)}{section.5}% 7
8\BOOKMARK [2][-]{subsection.5.3}{Installing PhyML on Microsoft Windows}{section.5}% 8
9\BOOKMARK [2][-]{subsection.5.4}{Installing the parallel version of PhyML}{section.5}% 9
10\BOOKMARK [1][-]{section.6}{Program usage.}{}% 10
11\BOOKMARK [2][-]{subsection.6.1}{PHYLIP-like interface}{section.6}% 11
12\BOOKMARK [3][-]{subsubsection.6.1.1}{Input Data sub-menu}{subsection.6.1}% 12
13\BOOKMARK [3][-]{subsubsection.6.1.2}{Substitution model sub-menu}{subsection.6.1}% 13
14\BOOKMARK [3][-]{subsubsection.6.1.3}{Tree searching sub-menu}{subsection.6.1}% 14
15\BOOKMARK [3][-]{subsubsection.6.1.4}{Branch support sub-menu}{subsection.6.1}% 15
16\BOOKMARK [2][-]{subsection.6.2}{Command-line interface}{section.6}% 16
17\BOOKMARK [2][-]{subsection.6.3}{XML interface}{section.6}% 17
18\BOOKMARK [2][-]{subsection.6.4}{Parallel bootstrap}{section.6}% 18
19\BOOKMARK [1][-]{section.7}{Inputs \046 outputs for command-line and PHYLIP interface }{}% 19
20\BOOKMARK [2][-]{subsection.7.1}{Sequence formats}{section.7}% 20
21\BOOKMARK [3][-]{subsubsection.7.1.1}{Gaps and ambiguous characters}{subsection.7.1}% 21
22\BOOKMARK [3][-]{subsubsection.7.1.2}{Specifying outgroup sequences}{subsection.7.1}% 22
23\BOOKMARK [2][-]{subsection.7.2}{Tree format}{section.7}% 23
24\BOOKMARK [2][-]{subsection.7.3}{Multiple alignments and trees}{section.7}% 24
25\BOOKMARK [2][-]{subsection.7.4}{Custom amino-acid rate model}{section.7}% 25
26\BOOKMARK [2][-]{subsection.7.5}{Topological constraint file}{section.7}% 26
27\BOOKMARK [2][-]{subsection.7.6}{Output files}{section.7}% 27
28\BOOKMARK [2][-]{subsection.7.7}{Treatment of invariable sites with fixed branch lengths}{section.7}% 28
29\BOOKMARK [1][-]{section.8}{Inputs \046 outputs for the XML interface }{}% 29
30\BOOKMARK [2][-]{subsection.8.1}{Mixture models in PhyML}{section.8}% 30
31\BOOKMARK [2][-]{subsection.8.2}{Partitions}{section.8}% 31
32\BOOKMARK [2][-]{subsection.8.3}{Combining mixture and partitions in PhyML: the theory}{section.8}% 32
33\BOOKMARK [2][-]{subsection.8.4}{The XML format and its use in PhyML}{section.8}% 33
34\BOOKMARK [2][-]{subsection.8.5}{Setting up mixture and partition models in PhyML: the basics}{section.8}% 34
35\BOOKMARK [2][-]{subsection.8.6}{XML options}{section.8}% 35
36\BOOKMARK [3][-]{subsubsection.8.6.1}{phyml component}{subsection.8.6}% 36
37\BOOKMARK [3][-]{subsubsection.8.6.2}{topology component}{subsection.8.6}% 37
38\BOOKMARK [3][-]{subsubsection.8.6.3}{ratematrices component}{subsection.8.6}% 38
39\BOOKMARK [3][-]{subsubsection.8.6.4}{equfreqs component}{subsection.8.6}% 39
40\BOOKMARK [3][-]{subsubsection.8.6.5}{branchlengths component}{subsection.8.6}% 40
41\BOOKMARK [3][-]{subsubsection.8.6.6}{siterates component}{subsection.8.6}% 41
42\BOOKMARK [3][-]{subsubsection.8.6.7}{partitionelem and mixtureelem components}{subsection.8.6}% 42
43\BOOKMARK [2][-]{subsection.8.7}{A simple example: GTR + 4 + I}{section.8}% 43
44\BOOKMARK [2][-]{subsection.8.8}{A second example: LG4X}{section.8}% 44
45\BOOKMARK [2][-]{subsection.8.9}{An example with multiple partition elements}{section.8}% 45
46\BOOKMARK [2][-]{subsection.8.10}{Branch lengths with invariants and partionned data}{section.8}% 46
47\BOOKMARK [1][-]{section.9}{Citing PhyML}{}% 47
48\BOOKMARK [1][-]{section.10}{Other programs in the PhyML package}{}% 48
49\BOOKMARK [2][-]{subsection.10.1}{PhyTime}{section.10}% 49
50\BOOKMARK [3][-]{subsubsection.10.1.1}{Installing PhyTime}{subsection.10.1}% 50
51\BOOKMARK [3][-]{subsubsection.10.1.2}{Running PhyTime}{subsection.10.1}% 51
52\BOOKMARK [3][-]{subsubsection.10.1.3}{Upper bounds of model parameters}{subsection.10.1}% 52
53\BOOKMARK [3][-]{subsubsection.10.1.4}{PhyTime specific options}{subsection.10.1}% 53
54\BOOKMARK [3][-]{subsubsection.10.1.5}{PhyTime output}{subsection.10.1}% 54
55\BOOKMARK [3][-]{subsubsection.10.1.6}{ClockRate vs. EvolRate}{subsection.10.1}% 55
56\BOOKMARK [3][-]{subsubsection.10.1.7}{Effective sample size}{subsection.10.1}% 56
57\BOOKMARK [3][-]{subsubsection.10.1.8}{Prior distributions of model parameters}{subsection.10.1}% 57
58\BOOKMARK [3][-]{subsubsection.10.1.9}{Citing PhyTime}{subsection.10.1}% 58
59\BOOKMARK [1][-]{section.11}{Recommendations on program usage}{}% 59
60\BOOKMARK [2][-]{subsection.11.1}{PhyML}{section.11}% 60
61\BOOKMARK [2][-]{subsection.11.2}{PhyTime}{section.11}% 61
62\BOOKMARK [1][-]{section.12}{Frequently asked questions}{}% 62
63\BOOKMARK [1][-]{section.13}{Acknowledgements}{}% 63
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