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REDHORSE Package
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| | Convert Merged Allele to Multiple Sequence Alignment fasta file | Index of Utilities
Analytical Pipeline | The
merged allele file which contains nucleotide information of parents as
well as hybrids not only facilitates comparison of hybrids against the
parents but also allows detection of double crossovers with reasonable
accuracy because of presence of physical location of the markers.
However, some of the recombination detection algorithms use multiple
sequence alignment fasta file as input. The convertMergedAllele2Fasta utility
in REDHORSE converts the merged allele file to multiple sequence
alignment file which can then be used as input to these programs.
Prerequisites1) Generate Input Data
2) Find Alleles
3) List Alleles
4) Find SNVs
5) Filter SNVs in close proximity (optional)
6) Consolidate SNVs (optional)
7) Generate a merged allele file
8) Retain biallelic loci and filter out loci with lots of missing data (optional)
How to run it?REDHORSE
takes the merged allele file as input and converts it into multiple sequence alignment file as follows:
java -jar
C:\AsisKhan\softwareManuscript\Code\REDHORSE.jar
convertMergedAllele2Fasta -i
C:\AsisKhan\softwareManuscript\data\mergedAllele_3.txt -o
C:\AsisKhan\softwareManuscript\data\mergedAllele_3.fasta
|
-i is merged allele file
-o is the output multiple sequence alignment file
OutputThe output of the program is a fasta file containing multiple sequence aligments
| Index of Utilities
Analytical Pipeline |
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