-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
COPYRIGHT
copyright 2011-2020 by the authors
MEGA has completed the requested action
Terminating the megacc process with exit code 0
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