megacc使用帮助说明书

-a --analysisOptions

MEGA Analysis Options File *required*

Specify the full path to the Mega Analysis Options (.mao) file.

This file tells MEGA-CC which analysis to perform as well as

which options to use

-c --calibration

Calibration file *optional*

Specify the full path to a calibration file that you wish to use. The calibration

file is used to provide calibration data for tree timing methods.

-ca --concatenate-alignments

Command to concatenate multiple sequence alignments into a single sequence alignment file

The files to be concatenated should either be located in a directory specified by the -d option

or the -l option can be used to specify the files to concatenate via a text file that has the

full path to each file on a separate line

-d --data

Data File *required*

Specify the full or relative path to the data file you wish to

analyze. MEGA (.meg), and Fasta files are supported for

all analyses. For distance matrices the MEGA (.meg) format is required.

-f --format *applies to sequence alignment only*

Export format for sequence alignment

Sequence alignments can be exported in either the native .meg

or FASTA format.

Format values:

MEGA

Fasta

-g --groups

Groups file *optional*

Specify the full path to the groups file that you wish to use. This file organizes

taxa into groups where each line in the file is a key value pair of the form

taxonName=groupName

Group information is used for certain analyses, for instance, specifying which taxon/taxa

comprise the outgroup for the timetree analysis

-gs --gap-symbol

The character that represents indels in the sequence data file that is being analyzed

If this is provided, it will override the value that is provided in the .mao file

-h --help

Help

Prints this help file document

-is --identical-base-symbol

The character that represents identical bases in the sequence data file that is being analyzed

If this is provided, it will override the value that is provided in the .mao file

-l --list

Input File List

Specifies a text file which has a list of input data files to be analyzed. This option can be used

instead of -d or -t to specify input data, in which case, the same analysis will be performed on all

input files listed in the text file and each output results files will be named using the name of

its corresponding input file. The indicated text file must be formatted such that each line has the

full path to the sequence data file to be used and if a tree file is also provided it is on the same

line but separated by a two pipe characters (e.g. || ). See EXAMPLES and LIST FORMAT below.

-ms --missing-base-symbol

The character that represents missing bases in the sequence data file that is being analyzed

If this is provided, it will override the value that is provided in the .mao file

-n --noSummary: Do not write out the analysis summary file

By default a file that gives an analysis summary is written.

This option suppresses the export of that file. However, if

any important messages are generated by the application, they

will be written to this file regardless.

-o --outfile *optional*

Output Path / Output Dir

Specify the full path and base filename (e.g. /myResultsDirectory/myResultName) or

simply the full path and directory of where to save the file

(e.g. /myResultsDirectory) in which case, a unique filename will be chosen

automatically for you.

-pfc --partition-frequency-cutoff

Partition Frequency Cutoff (a value between 0.0 and 1.0 - default is 0.5) *optional*

When bootstrapping is used for tree construction a list of partitions and

frequencies is written to a text file. The partition frequency cutoff

causes any partitions whose frequency is less than the cutoff value

to be ommited from this text file. Set this value to 0.0 to include

all partitions.

-r --recursive

Recursive directory search *optional*

If a directory is specified for analysis by default MEGA only searches

the contents of that folder and not any of it's children. To include the

contents of all folders under the one specified, use this option.

-s --silent: Do not write out the progress updates

This option prevents progress updates from being written to stdout.

-t --tree *required for some analyses*

Tree File

Specify the full path to the tree file you wish to use. (Some

analyses requires a user provided tree, or allow you to provide

your own)

If no output path is specified, results will be saved in the same directory

as the input data file, with a unique name.

EXAMPLES

This example performs a multiple sequence alignment on codons (it assumes that you have created

the file "Clustal_Codon_Alignment.mao" using the prototyper (megaproto). A fasta file with coding

data is used as input and the resulting alignment is output

in the MEGA format:

megacc -a ~/Documents/Clustal_Codon_Alignment.mao -d ~/Documents/codingData.fas -o ~/Documents/codingDataAligned.meg

This example shows how to construct a neighbor-joining phylogeny for each of a list of sequence data files.

The analysis will be performed for each file listed in "listOfDataFiles.txt" and all results will be written to

the ~/Documents/outputDirectory/ directory:

megacc -a ~/Documents/NJ_Tree_Settings.mao -l ~/Documents/listOfDataFiles.txt -o ~/Documents/outputDirectory/

LIST FORMAT

When using the -l option, each file to be analyzed must be on its own line. For example:

~/Documents/myData/seqData1.fas

~/Documents/myData/seqData2.fas

~/Documents/myData/seqData3.fas

If the analyses are to use a user-provided Newick tree file, then the tree files are given on the same line as

the data files, following two pipe characters. For example:

~/Documents/myData/seqData1.fas || ~/Documents/myData/treeFile1.nwk

~/Documents/myData/seqData2.fas || ~/Documents/myData/treeFile2.nwk

~/Documents/myData/seqData3.fas || ~/Documents/myData/treeFile3.nwk

CALIBRATION FORMAT

For the Reltime analysis, multiple calibration points can be used to convert relative times to absolute

times. Calibrations are given in a text file which is specified using the -c option and is formatted using

one of three formats. In the first format, the node in the tree for a given calibration is specified

by its name, which must be included as an internal node label in the newick tree file used:

!NodeName1="name1" minTime=1.75 maxTime=2.25;

!NodeName2="name2" minTime=3.0;

!NodeName3="name3" time=2.5;

In the second format, the node in the tree for a given calibration point is indicated by specifying two

taxa whose most recent common ancestor is the node to calibrate:

!MRCA="some name1" TaxonA="taxon1 name" TaxonB="taxon2 name" minTime=1.75 maxTime=2.25;

!MRCA="some name2" TaxonA="taxon3 name" TaxonB="taxon4 name" minTime=3.0;

!MRCA="some name3" TaxonA="taxon5 name" TaxonB="taxon6 name" time=2.5;

In the third format, target nodes are specified in the same way as the above examples but

probability distributions are specifed for divergence time constraints instead of min and max times:

!NodeName1="name1" Distribution=normal mean=6.4 stddev=1.2;

!MRCA="some name2" TaxonA="taxon1 name" TaxonB="taxon2 name" Distribution=exponential time=8.2 lambda=0.25;

!MRCA="some name3" TaxonA="taxon1 name" TaxonB="taxon2 name" Distribution=uniform mintime=4 maxtime=6;

!MRCA="some name4" TaxonA="taxon1 name" TaxonB="taxon2 name" Distribution=lognormal offset=7.0 mean=2.38 stddev=0.15;

CITING MEGACC

Kumar S, Stecher G, Peterson D, and Tamura K (2012) MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis. Bioinformatics 28:2685-2686.

Kumar S, Stecher G, Li M, Knyaz C, and Tamura K (2018) MEGAX: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35:1547-1549.

AUTHORS

Sudhir Kumar, Glen Stecher, and Koichiro Tamura

MEGA has completed the requested action

Terminating the megacc process with exit code 0