source: branches/lib/GDEHELP/HELP_WRITTEN/raxml8.help

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
File size: 6.5 KB
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1RAxML 8 (DNA)
2
3DESCRIPTION
4
5        RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum
6        Likelihood-based inference of large phylogenetic trees.
7
8        It has originally been derived from fastDNAml which
9        in turn was derived from Joe Felsenteins dnaml which is part of the PHYLIP package.
10
11        Author: Alexandros Stamatakis
12
13        http://sco.h-its.org/exelixis/web/software/raxml/index.html
14
15        Original RAxML documentation can be found at
16        http://sco.h-its.org/exelixis/php/countManualNew.php
17
18        Several parts of this documentation have been used here.
19
20        Version distributed with ARB and used by this window: RAxML 8.2.8
21
22PARAMETERS
23
24        Only the parameters adjustable via the ARB interface are described below.
25        For in-depth documentation please refer to original documentation
26        (the main used raxml options are specified for each protocol).
27
28
29          Input tree
30
31            Not required/used for tree reconstruction protocols 'Thorough' and 'Quick'.
32
33          Protocol
34
35            The following protocols are defined in ARB RAxML8 interface:
36
37              Thorough tree search ("-f d")
38
39                1. perform multiple searches for the best ML tree (uses "new rapid hill-climbing")
40                2. (optionally) perform multiple bootstrap searches (executed parallel to 1. if enough CPU cores available)
41                3. draw bipartition information (from 2.) on best tree found in 1.
42
43              Quick tree search ("-f a")
44
45                Rapid bootstrap analysis and search for best-scoring ML tree in one raxml run.
46
47              Add to tree ("-g")
48
49                Add species to specified input tree w/o modifying the trees topology.
50                You need to mark all species which are member of the input tree,
51                plus the species you like to add to that tree.
52                The resulting tree will be imported into a new tree.
53
54                If bootstrapping is selected, steps 2. and 3. from Thorough-protocol are executed.
55
56              Optimize tree ("-f t")
57
58                Perform randomized tree searches on one fixed starting tree.
59                Imports the best resulting tree into ARB.
60
61                If bootstrapping is selected, steps 2. and 3. from Thorough-protocol are executed.
62
63              Calculate branchlengths ("-f e")
64
65                Similar to 'Score tree', but also calculates new branchlengths
66                and reimports the tree (as new tree).
67
68                If bootstrapping is selected, steps 2. and 3. from Thorough-protocol are executed.
69
70              Calculate bootstraps ("-b")
71
72                Perform multiple bootstrap searches on marked species.
73                Draw bipartition information on input tree and import as
74                new tree.
75
76              Score tree ("-f n")
77
78                Calculates the likelihood for the specified input tree and
79                appends the result to the comment of the existing tree.
80
81                If you like to compare the likelihoods of different trees,
82                please note that these depend (at least) on the
83                following conditions:
84                  * set of sequences (=which species are members of the trees)
85                  * used Model
86                  * used Filter
87
88          Model
89
90            The following substitution models are provided in ARB RAxML8 interface:
91
92                GTRCAT
93
94                  GTR + Optimization of substitution rates + Optimization of
95                  site-specific evolutionary rates which are categorized into
96                  numberOfCategories distinct rate categories for greater
97                  computational efficiency.
98
99                GTRGAMMA
100
101                  GTR + Optimization of substitution rates + GAMMA model of
102                  rate heterogeneity (alpha parameter will be estimated).
103
104          Searches
105
106            Specifies the number of searches for best ML tree that will
107            be performed in step 1. of 'Thorough' protocol and
108            the number of randomized searches performed
109            in 'Optimize tree' protocol.
110
111          Bootstraps
112
113            Specifies the number of bootstrap runs to perform.
114
115             * 'No' disables bootstrapping (not possible for 'Quick' protocol).
116             * 'Auto' uses RAxML8 option '-N autoMRE_IGN'
117             * or explicitely select number of runs to perform.
118
119          Compute MRE consensus tree
120
121            Compute extended majority rule consensus tree from bootstrapped trees.
122
123          Tree name
124
125            Suffix for result tree(s) loaded into ARB, e.g.:
126
127                'raxml' => 'tree_raxml' (and optionally 'tree_raxml_mre' if MRE tree requested)
128
129          Random seed
130
131                Specifies a fixed random seed (used for parsimony inferences AND rapid bootstrapping).
132                This only makes sense if you like to reproduce results (which isn't possible for all cases).
133
134                Recommended default setting is (empty). The number of seconds
135                since 'epoch' will be used in that case.
136
137          CPU thread override
138
139                Specify number of threads to use (for bootstrapping and ML search).
140
141                The script tries to detect the number of CPU cores available.
142                If it fails to detect the (correct) number of cores on your machine, you
143                can set the environment variable PBS_NP to the number of cores available.
144
145                If the number of threads is not specified (=empty, which is recommended),
146                the script will check the input alignment and automatically select the
147                number of threads to use.
148
149                If there are at least twice as many cores as threads wanted (approx.),
150                bootstrapping and ML search will run asynchronously.
151                Otherwise they run one after the other.
152
153                When specifying the number of threads manually, make sure you do not specify
154                more threads than cores available on your hardware, otherwise you'll encounter
155                a massive performance penalty!
156
157                If you like to force asynchronous execution of bootstrapping and ML search,
158                set thread override to CORES/2 (e.g. if you have 8 cores select 4 threads).
159
160                If you like to force sequential execution of bootstrapping and ML search, set
161                the number of cores to a higher value. Please note that selecting too many threads
162                may also result in degraded performance.
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