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fastdnaml_1.2.2.yaml
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fastdnaml_1.2.2.yaml
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!mobyle/program
name: fastdnaml
version: 1.2.2
title: fastDNAml
description: Construction of phylogenetic trees of DNA sequences using maximum likelihood
authors: Olsen, Matsuda, Hagstrom, Overbeek
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
format: ("fastDNAml", "cat > %s.tmp;" % infile )[bootstrap]
argpos: 1000
name: fastdnaml
command: true
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '" && clean_checkpoints"'
argpos: 1100
name: clean_tmp
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: The input to fastDNAml is similar to that used by DNAML (and the
other PHYLIP programs). At least 3 sequences are required.
prompt: Sequence Alignment File
format: '"cat " + str(value) + " | "'
simple: true
argpos: 1
mandatory: true
name: infile
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1955']
data_terms: ['EDAM_data:1383']
- !mobyle/inputprogramparagraph
prompt: Input Options
name: inputopt
children:
- !mobyle/inputprogramparameter
prompt: Use empirical base frequencies derived from the sequence data
?
format: ( "" ,"frequencies %s %s %s %s | " % (str(fA), str(fC), str(fG),
str(fT)) )[ not ( value and fA is None and fC is None and fG is None
and fT is None) ]
argpos: 2
name: frequencies
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: User bases frequencies (instead of empirical frequencies)
name: user_frequencies
precond: {'#not': frequencies}
children:
- !mobyle/inputprogramparameter
prompt: A frequency
mandatory: true
name: fA
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
prompt: C frequency
mandatory: true
name: fC
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
prompt: G frequency
mandatory: true
name: fG
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
prompt: T frequency
mandatory: true
name: fT
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
comment: This option can be used before a global or treefile option with
auxiliary data.
prompt: Transition/transversion ratio
format: ( "" , " transition " + str(value) + " | " )[ value is not None
and value != vdef]
argpos: 10
name: transition
command: false
type: !mobyle/floattype {default: 2.0}
- !mobyle/inputprogramparameter
comment: "Note that fastDNAml explores a very small number of alternative\
\ tree topologies relative to a typical parsimony program. There is\
\ a very real chance that the search procedure will not find the tree\
\ topology with the highest likelihood. Altering the order of taxon\
\ addition and comparing the trees found is a fairly efficient method\
\ for testing convergence. Typically, it would be nice to find the\
\ same best tree at least twice (if not three times), as opposed to\
\ simply performing some\n fixed number of jumbles and\
\ hoping that at least one of them will be the optimum."
prompt: Randomize input order of sequences (jumble)
format: ( "" , "jumble | " )[ value ]
argpos: 10
name: jumble
precond: {'#not': bootstrap}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: The G (global) option has been generalized to permit crossing
any number of branches during tree rearrangements. In addition, it
is possible to modify the extent of rearrangement explored during
the sequential addition phase of tree building.The G U (global and
user tree) option combination instructs the program to find the best
of the user trees, and then look for rearrangements that are better
still.If a rearrangement distance is specified, the input must contain
a transition option.The Global option can be used to force branch
swapping on user trees, (combination of Global and User Tree(s) options).
prompt: Global rearrangements
format: ( "" , " global ")[ value ]
argpos: 11
name: global_opp
precond:
'#or':
- transition: {'#ne': None}
- bootstrap
- jumble
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Number of branches to cross in rearrangements of the completed
tree
format: ( "" , " %s " % str(final_arrgt))[ value is not None]
argpos: 12
name: final_arrgt
precond:
'#and':
- '#or':
- transition: {'#ne': None}
- bootstrap
- jumble
- global_opp
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Number of branches to cross in testing rearrangements during the
sequential addition phase of tree inference
format: ( "" , " %s " % str(partial_arrgt))[ value is not None]
argpos: 13
name: partial_arrgt
precond:
'#and':
- '#or':
- transition: {'#ne': None}
- bootstrap
- jumble
- global_opp
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Number of branches to cross in testing rearrangements during the
sequential addition phase of tree inference
format: '" | "'
argpos: 14
name: pipe_arrgt
precond:
'#and':
- '#or':
- transition: {'#ne': None}
- bootstrap
- jumble
- global_opp
command: false
hidden: true
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
comment: This option greatly decreases the time in initially placing a
new sequence in the growing tree (but does not change the time required
to subsequently test rearrangements). The overall time savings seems
to be about 30%, based on a very limited number of test cases. Its
downside, if any, is unknown. This will probably become default program
behavior in the near future.If the analysis is run with a global option
of 'G 0 0', so that no rearrangements are permitted, the tree is build
very approximately, but very quickly. This may be of greatest interest
if the question is, 'Where does this one new sequence fit into this
known tree?' The known tree is provided with the restart option, below.PHYLIP
DNAML does not include anything comparable to the quickadd option.
prompt: Decreases the time in initially placing a new sequence in the
growing tree (quickadd)
format: ( "" , " quickadd | " )[ value ]
argpos: 2
name: quickadd
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Use the specified sequence number as outgroup
format: ( "" , "outgroup " + str(value) + " | " )[ value is not None ]
argpos: 2
name: outgroup
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparagraph
comment: This options allows you to enter your own trees and instructs the
program to evaluate them.
prompt: User input Tree Options
name: treeopt
precond: {'#not': bootstrap}
children:
- !mobyle/inputprogramparameter
comment: The trees must be in Newick format, and terminated with a semicolon.
(The program also accepts a pseudo_newick format, which is a valid
prolog fact.)The tree reader in this program is more powerful than
that in PHYLIP 3.3. In particular, material enclosed in square brackets,
[ like this ], is ignored as comments; taxa names can be wrapped in
single quotation marks to support the inclusion of characters that
would otherwise end the name (i.e., '(', ')', ':', ';', '[', ']',
',' and ' '); names of internal nodes are properly ignored; and exponential
notation (such as 1.0E-6) for branch lengths is supported.
prompt: User tree - tree(s) file
format: ( "" , " usertree %s |" % str(value) )[ value is not None ]
argpos: 2
name: user_tree
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1910']
data_terms: ['EDAM_data:0872']
- !mobyle/inputprogramparameter
comment: Causes user trees to be read with branch lengths (and it is an
error to omit any of them). Without the L option, branch lengths in
user trees are not required, and are ignored if present.
prompt: User trees to be read with branch lengths
format: ( "" , "userlengths |" )[ value ]
argpos: 2
name: user_lengths
precond: {'#not': bootstrap}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Bootstrap
name: boot
children:
- !mobyle/inputprogramparameter
comment: Tree files will be summarized in one '.tree' file as well as
output files in one '.out' file
prompt: Generates a re-sample of the input data (bootstrap)
format: ( "" , " fastdnaml " )[ value ]
simple: true
argpos: 1001
name: bootstrap
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Bootstrap options
name: bootopt
precond: bootstrap
children:
- !mobyle/inputprogramparameter
prompt: Number of different bootstrap samples
format: ( "" , " -boots " + str(value) )[ value is not None and value
!= vdef]
simple: true
argpos: 1002
name: nboots
command: false
type: !mobyle/integertype {default: 1}
- !mobyle/inputprogramparameter
comment: 'Warning: For a given random number seed, the sample will
always be the same.'
prompt: Random number seed for first bootstrap
format: ( "" , " -seed " + str(value) )[ value is not None ]
simple: true
argpos: 1002
name: bootstrap_seed
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Maximum attempts at replicating inferred tree (max jumble)
format: ( "" , " -jumble " + str(value) )[ value is not None and value
!= vdef]
argpos: 1002
name: bootstrap_maxjumble
precond: bootstrap
command: false
type: !mobyle/integertype {default: 10}
- !mobyle/inputprogramparameter
format: '" %s.tmp" % str(infile)'
argpos: 1003
name: in_bootfile
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Output and Results Options
name: output_opt
children:
- !mobyle/inputprogramparameter
prompt: Output File
format: ( "" , " > " + str(outfile) )[ value is not None ]
argpos: 1010
name: outfile
precond: {'#not': bootstrap}
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Save tree in treefile
format: ( "treefile | ", "" )[ value ]
argpos: 2
name: treefile
precond: {'#not': bootstrap}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Print the input alignment at start of run (printdata)
format: ( "" , "printdata | " )[ value ]
argpos: 2
name: printdata
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Categories and Weights Options
name: categopt
children:
- !mobyle/inputprogramparameter {comment: "The data must have the format specified\
\ for PHYLIP dnaml 3.3. The first line must be the letter C, followed\
\ by the number of categories (a number in the range 1 through 35),\
\ and then a blank-separated list of the rates for each category.\
\ (The list can take more than one line; the program reads until it\
\ finds the specified number of rate values.) The next line should\
\ be the word Categories followed by one rate category character per\
\ sequence position. The categories 1 - 35 are\n represented\
\ by the series 1, 2, 3, ..., 8, 9, A, B, C, ..., Y, Z. These latter\
\ data can be on one or more lines. For example:C 12 0.0625 0.125\
\ 0.25 0.5 1 2 4 8 16 32 64 128Categories 5111136343678975AAA8949995566778888889AAAAAA9239898629AAAAA9Category\
\ 'numbers' are ordered: 1, 2, 3, ..., 9, A, B, ..., Y, Z. Category\
\ zero (undefined rate) is permitted at sites with a zero in a user-supplied\
\ weighting mask.", prompt: Rate categories file (user-specified),
format: '( "" , "categories "+ str(value) + " |" )[ value is not None
]', argpos: 2, name: categories, command: false}
- !mobyle/inputprogramparameter {comment: 'example:Weights 111111111111001100000100011111100000000000000110000110000000In
case of bootstrap, only positions that have nonzero weights are used
in computing the bootstrap sample.', prompt: Weights file (user-specified
column weighting information), format: '( "" , "weights " + str(value)
+ " |" )[ value is not None ]', argpos: 2, name: weights, command: false}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output and Results Options
name: output_opt
children:
- !mobyle/outputprogramparameter
prompt: Output(s) file
filenames: '"fastdnaml.out"'
name: outputfile
precond:
'#and':
- {'#not': bootstrap}
- outfile: {'#eq': None}
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Output(s) file
filenames: str(outfile)
name: outputfile_name
precond:
'#and':
- {'#not': bootstrap}
- outfile: {'#ne': None}
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Tree file
filenames: '"_treefile.[0-9]*"'
name: treefiles
precond: {'#not': bootstrap}
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1910']
data_terms: ['EDAM_data:0872']
- !mobyle/outputprogramparameter
prompt: Bootstrap output report
filenames: '"%s.tmp.out" % str(infile)'
name: bootstrap_report
precond: bootstrap
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Bootstrap tree file
filenames: '"%s.tmp.tree" % str(infile)'
name: bootstrap_tree
precond: bootstrap
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1910']
data_terms: ['EDAM_data:0872']
- !mobyle/outputprogramparameter
prompt: Bootstrap alignment file
filenames: '"%s.tmp" % str(infile)'
name: bootstrap_aln
precond: bootstrap
type: !mobyle/formattedtype
data_terms: ['EDAM_data:0863']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"fastdnaml.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: 'Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994.
fastDNAml: A tool for construction of phylogenetic trees of DNA sequences
using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.', url: null}
- {doi: null, label: 'Felsenstein, J. 1981. Evolutionary trees from DNA sequences:
A maximum likelihood approach. J. Mol. Evol. 17: 368-376.', url: null}
homepage_links: ['http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html']
env: {}