Description of Applications
This document contains a list of the applications in ANDES grouped by function.
All scripts will report their usage and parameters when invoked without any parameters specified.
Scripts that perform comparisons or merging, will automatically invoke Clustalw2, so it is important that you already have it installed.
See the Examples page for a few working examples you can try with the data provided with the download package.
Profile Generation
Generate a Position Profile from a Clustalw Output file:
ClustalALN_to_PositionProfile.pl
Generate a Position Profile from a reference FASTA file:
FASTA_to_PositionProfile.pl
Generate a Distance Matrix amongst all the sequences in a Clustalw Output file:
ClustalALN_to_RDistanceMatrix.pl
Inter Profile Comparison
Generate a Distance Matrix amongst all the Position Profiles you specify:
Compare_PositionProfiles_to_RDistanceMatrix.pl
Generate a Base Conversion table based on the two Position Profiles you specify:
Compute_BaseConversion_Tables.pl
Generate a Position-by-position RMSD Difference from a Reference Position Profile for each Query Position Profile.
Compute_DiffFromRef_PositionProfile_per_position.pl
Intra Profile Analysis
Compute the number of Gaps in Position Profile and the length of the base that preceded it. This is potentially useful for trying to attribute homopolymer attribution to 454 sequencing indel errors.
Compute_Gap_Analysis.pl
Compute the %GC content vs Variation across the length of the profile. This is potentially useful for determining if there are any correlations between sequencing error/variation and %GC content.
Compute_GCContent_vs_Variation_on_Profile.pl
Compute the Normalized Shannon Entropy across the length of a profile:
Compute_NormalizedShannonEntropy_for_Profile.pl
Compute the QV across the length of a profile (Assumes reads are clonal and all difference are from PCR or sequencing error):
Compute_QV_for_Profile.pl
Miscellaneous Profile Tools
Filters variations from a Position Profile based on user-supplied thresholds:
Filter_Profile_By_Threshold.pl
Filter deeply gapped positions from the Position Profile:
Filter_Profile_Gaps.pl
Merge multiple Position Profiles together into a new Position Profile:
Merge_PositionProfiles.pl
Convert Position Profile to a Multi-FASTA file based on the most common allele at each position:
Profiles_To_Multifasta.pl
Convert a Position Profile to a Consensus FASTA file using ambiguity codes where there are mixed bases.
Profile_To_ConsensusFASTA.pl
Graphical Tools (R scripts for plotting results)
Produce a dot plot based on the output from comparing multiple profiles against a reference profile (Compute_DiffFromRef_PositionProfile_per_position.pl). This will help you visualize which positions are significantly different between the reference and all the profiles.
Plot_PositionProfile_From_Reference.r
Produce a Dendrogram and MDS plot given a Distance Matrix from ClustalALN_to_RDistanceMatrix.pl or Compare_PositionProfiles_to_RDistanceMatrix.pl
QuickPlot_DistanceMatrix.r