Template Batch Files

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Batch Files (0-9,A-M)

Filename Subfolder Brief description Comments Status
454 (source) Alignment and filtering indel errors for Roche/454 deep sequencing data Needs major refactoring and updating. Could be deprecated because of Lance's Python module
AAModelComparison (source) Automated model selection for amino acid substitution rates Fairly clean. Should be tweaked to read the list of available models at runtime.
AnalyzeCodonData (source) Fit a codon substitution model to nucleotide sequences. Can constrain with by a global scaling factor so that branch lengths remain congruent to user-specified tree. Should be rolled into a new: FitModelToFixedTree file.
AnalyzeCodonDataMPI (source) Creates a fixed number of codon partitions, but then fits an F81 (nucleotide) model. No actual MPI-enabled functionality. Does not work as advertised. Terminate with extreme prejudice. Terminate
AnalyzeDiNucData (source) Partitions alignment into dinucleotide characters (grouping every two nucleotides). Fits one of several dinucleotide-specific template models such as Muse (1995). Should be rolled into a new: FitModelToFixedTree file.
AnalyzeNucDataFreq (source) Estimates and reports equilibrium nucleotide frequencies by fitting template nucleotide model to sequence data and tree. Reports observed nucleotide frequencies for comparison. No documentation. Does GetString() on TrNModel at end of file for no apparent reason. Uses EMBED_FREQUENCY_DEPENDENCE flag which appears to be deprecated. Should be rolled into a new: FitModelToFixedTree file.
AnalyzeNucDataFreq2 (source) Estimates and reports nucleotide frequencies at root and equilibrium frequencies. Similar to AnalyzeNucDataFreq with same issues. Passes 3 arguments to LikelihoodFunction which I've never seen before. Suspect this file is outdated. Terminate
AnalyzeNucProtData (source) Fits a template nucleotide or amino acid model to sequence data and tree. Should be rolled into a new: FitModelToFixedTree file.
AnalyzeNucProtData2 (source) Same as AnalyzeNucProtData; also reports tree length and transition matrix at first tip of tree. Broken. If run on nucleotide data then rate matrix extracted from tree node will be 4x4 not 20x20, causing indexing error at line 48. If run on AA data, vectorOfFrequencies not defined in template AA model, causing indexing error in same line. Recommend kill. Terminate
BGM (source) Collection of functions for applying Bayesian graphical models to ancestral sequence reconstructions. Limited MPI functionality for sampled ancestral reconstrcutions. BGM class undergoing extensive revision. Needs assignment
BivariateCodonRateAnalysis (source) Fit codon substitution models with increasing number of paired non-synonymous and synonymous rate classes, using a greedy search heuristic that resembles coordinate descent. Needs documentation. Requires CodonBivariateRateProcessor.bf to process results. Needs assignment
BranchClassDNDS (source) Fit codon substitution model with different methods for handling rate variation across sites, given a fixed number of rate classes. Allocates branch classes to rate classes. In a nutshell, tests the hypothesis of whether different branches in the tree are evolving at different rates with respect to dN and/or dS. Requires a branch splits file. Needs documentation. Needs assignment
BranchSiteREL (source) Find lineages episodic selection (accelerated rate of non-synonymous substitution) using random effects model. Initially fits local MG94 model, then evaluates every branch for which one dN/dS rate class exceeds 1 with weight exceeding machine precision. Tests this result against an alternative model where the rate class is set to dN/dS=1 for this branch. Phase 1 commented out. Analysis skips from phase 0 directly to phase 2. Needs assignment
BranchSwap (source) Use nearest-neighbour interchange algorithm on user-specified tree to attempt to find maximum likelihood tree. Not recommended for large trees. Needs assignment
branchSwappingFunctions (source) Collection of functions used for branch swap-based heuristic search algorithms for maximum likelihood tree. Should be reclassified as an include (.ibf) file. Needs assignment
BS2007 (source) Branch-site model. Determine whether site-specific dN/dS rates are significantly different at one or more branches of a tree relative to the background using random-effects likelihood approach. Finally, some documentation! Needs assignment
categoryEcho (source) Post-processing utility file. Report and/or display results when fitted model included rate class variables (categories). Needs assignment
CF3x4 (source) TemplateModels Needs assignment
CleanGaps (source) Filter columns from a nucleotide sequence alignment where the proportion of sequences with gaps at that position exceeds a user-defined threshold. Needs assignment
CleanStopCodons (source) Filter stop codons (determined by genetic code) from a codon sequence alignment. Also filter columns comprised entirely of gaps and/or duplicate sequences. Needs assignment
ClusterAnalysis (source) Generate a tree from a sequence alignment using one of several clustering methods (e.g., UPGMA, unweighted pair group methods with arithmetic mean). Maximum likelihood estimation of pairwise distances. Produces trees with global molecular clock. Needs assignment
ClusterByDistanceRange (source) Cluster sequences using a user-specified pairwise distance matrix and cutoff value. Can write out results as GraphViz (DOT format) file. Needs assignment
CodonBivariateRateProcessor (source) Post-processing of models fitted by BivariateCodonRateAnalysis.bf. Chart windows display distribution of dN and dS rates, and posterior rate class assignments by codon site. Needs assignment
CodonModelCompare (source) Evaluate the fit of all 203 time-reversible models of nucleotide substitution in the framework of the MG94 codon substitution model, given an alignment of codon sequences. Select the best-fitting model based on AIC. Needs assignment
CodonToProtein (source) Translates codon sequences into protein sequences. Maps codons containing gaps or fully-ambiguous nucleotides ("N") to residues if all resolutions are synonymous. Does not handle IUPAC nucleotide mixtures (WRYKSMBDHV). Needs assignment
CodonUsageBias (source) Needs assignment
CompareSelectivePressure (source) Test whether sites in two populations are evolving under different selective pressures. Needs assignment
CompareSelectivePressureIVL (source) Test whether sites in two populations are evolving under different selective pressures along internal tree branches. I suspect this could be rolled into CompareSelectivePressure. Needs assignment
ConvertDataFile (source) Read a sequence data file and convert it into another format (FASTA, PHYLIP, NEXUS) Essentially a wrapper for DATA_FILE_PRINT_FORMAT. Does not really serve any function that cannot be accomplished with the GUI. Consider kill. Needs assignment
discreteGenerator (source) 2RatesAnalyses Initialize a general discrete distribution of dN and dS rates. Called by [[dNdSRateAnalysis|dNdSRateAnalysis.bf] Should have .def extension and not .bf Needs assignment
discreteGeneratorNoPS (source) 2RatesAnalyses Similar to discreteGenerator but adds constraint of dN <= dS. Provides null model to assess presence of selection. Should have .def extension and not .bf Needs assignment
DatedTipsMolecularClock (source) Test for presence of global molecular clock using dated sequences. Estimates rates and dates for internal nodes. Implementation and extension of Andrew Rambaut's TipDate program. Needs assignment
DirectionalREL (source) Fit a random effects model to detect directional selection towards a particular residue at sites of a protein sequence alignment. Art - I added comments throughout this batch file some time ago when I was trying to make sense of it :) Needs assignment
DirectionalREL_MF (source) Needs assignment
DistanceMatrix (source) Generate a pairwise distance matrix for a sequence alignment using a predefined distance metric (e.g., K2P) or by maximum likelihood. Matrix output in one of four formats (PHYLIP, HBL, tab-delimited, and pairwise). MPI-enabled. Needs assignment
DistanceMatrix_Splits (source) Generate pairwise distance matrices for a sequence alignment in a sliding window of user-defined width. Output only in PHYLIP and HBL formats. Needs assignment
distanceMethodNPBootstrap (source) A collection of support functions for NeighborJoining. Needs to be reclassified as an *.ibf file, and suggest rename to NeighborJoining.ibf. Alternatively, merge with distanceRMethodNPBootstrap.bf because of overlap in functionality. Needs assignment
distanceRMethodNPBootstrap (source) A collection of support functions for ClusterAnalysis.bf Similarly, recommend renaming to ClusterAnalysis.ibf. Needs assignment
dNdSBivariateRateAnalysis (source) Fits a codon substitution model to two or more sequence alignments (not necessarily homologous) for inferring bivariate rate classes. Likelihood function evaluates both data sets simultaneously. Presumably differences between the sequence alignments are evaluated from the joint distribution of rate classes in single model fit. No documentation. Needs assignment
dNdSBivariateRateAnalysis_CompareDS (source) Fit codon substitution models to two or more sequence alignments (not necessarily homologous) and compare distribution across sites of synonymous rate categories. Probably developed for ESD project. Contains a bug on line 170: "modelDesc" used without being defined, should be "modelDesc1", i.e., model specification string for data set 1. Appears to be broken. Needs assignment
dNdSDistributionComparison (source) Needs assignment
dNdSDistributionComparisonMF (source) Needs assignment
dNdSDistributionComparisonPartitions (source) Needs assignment
dNdSRateAnalysis (source) Needs assignment
dNdSRateAnalysis_MF (source) Needs assignment
dNdSResultProcessor (source) Needs assignment
doNNISwap (source) Needs assignment
doSPRSwap (source) Needs assignment
F_ST (source) Needs assignment
FitnessAAModels (source) Needs assignment
GADatedClock (source) Needs assignment
GADatedClockProcessor (source) Needs assignment
GADatedClockProcessorM (source) Needs assignment
GARD (source) Needs assignment
GARDProcessor (source) Needs assignment
GARecomb (source) Needs assignment
Gateaux (source) Needs assignment
Gateaux2 (source) Needs assignment
GateauxMR (source) Needs assignment
heuristicMethodNPBootstrap (source) Needs assignment
Kernel_k_means (source) Needs assignment
Kernel_PCA (source) Needs assignment
KHTest (source) Needs assignment
lhc (source) Samplers Needs assignment
LHT (source) Needs assignment
LocalBranchSiteTest (source) Needs assignment
LocalMolClock (source) Needs assignment
LRTRecombTest (source) Needs assignment
LZ_Complexity (source) Needs assignment
MaxChi2 (source) Needs assignment
MEDS (source) Needs assignment
MergeSequences (source) Needs assignment
MergeSites (source) Needs assignment
MFPositiveSelection (source) Needs assignment
MFPositiveSelectionPooled (source) Needs assignment
MGvsGY (source) Needs assignment
ModelSelectorAAProcessor (source) Needs assignment
ModelSelectorBranch (source) Needs assignment
ModelSelectorCodon (source) Needs assignment
ModelSelectorCodonProcessor (source) Needs assignment
ModelSelectorRNA (source) Needs assignment
ModelSelectorRNA_1 (source) Needs assignment
ModelTest (source) Needs assignment
MolClockAllRoots (source) Needs assignment
molclockBootstrap (source) Needs assignment
MolecularClock (source) Needs assignment
AncestralMapper (source) Utility Needs assignment
CoalescentPostProcessor (source) Utility Needs assignment
CodonTools (source) Utility Needs assignment
DescriptiveStatistics (source) Utility Needs assignment
GrabBag (source) Utility Needs assignment
HXB2Mapper (source) Utility Needs assignment
LocalMGREV (source) Utility Needs assignment
LocalMGREVMLFreqs (source) Utility Needs assignment
MPITools (source) Utility Needs assignment
Filename Subfolder Brief description Comments Status

Batch Files (N-Z)

Filename Subfolder Brief description Comments Status
NeighborJoining (source) Needs assignment
NielsenYang (source) Needs assignment
NucModelCompare (source) Needs assignment
PairwiseDNDS (source) Needs assignment
PairwiseRelativeRate (source) Needs assignment
PairwiseRelativeRatio (source) Needs assignment
PairwiseSiteDiversity (source) Needs assignment
PARRIS (source) Needs assignment
PartitionDataFile (source) Needs assignment
PartitionRateComparison (source) Needs assignment
Phylohandbook (source) Needs assignment
Plato (source) Needs assignment
PositiveSelectionLI (source) Needs assignment
post_ancestors (source) Needs assignment
post_counting (source) Needs assignment
post_covariance (source) Needs assignment
post_dNdS (source) Needs assignment
post_lfprofile (source) Needs assignment
post_npbs (source) Needs assignment
post_pbs (source) Needs assignment
post_sampler (source) Needs assignment
post_saveResults (source) Needs assignment
post_sns (source) Needs assignment
post_variance (source) Needs assignment
post_viewResults (source) Needs assignment
queryTree (source) Needs assignment
QuickSelectionDetection (source) Needs assignment
QuickSelectionDetectionMF (source) Needs assignment
RateClassCounter (source) Needs assignment
readIndexFile (source) Needs assignment
ReduceDataSetMatrix (source) Needs assignment
RelativeRate (source) Needs assignment
RelativeRateL (source) Needs assignment
RelativeRatio (source) Needs assignment
relrateBootstrap (source) Needs assignment
relrateBootstrapL (source) Needs assignment
relratioBootstrap (source) Needs assignment
SampleProcessor (source) Needs assignment
sir (source) Samplers Needs assignment
SandNSAmbigs (source) Needs assignment
SelectionLRT (source) Needs assignment
selectModelParameters (source) Needs assignment
SeqAlignment (source) Needs assignment
SeqAlignmentCodon (source) Needs assignment
SeqAlignmentNuc (source) Needs assignment
SeqAlignmentProt (source) Needs assignment
SeqAlignmentTop75 (source) Needs assignment
SequentialAddition (source) Needs assignment
SGASimProcessor (source) Needs assignment
SGEmulator (source) Needs assignment
SGEmulator_MF (source) Needs assignment
SGIvL (source) Needs assignment
SimilarityPlot (source) Needs assignment
SimmondsAI (source) Needs assignment
simpleBootstrap (source) Needs assignment
SimpleMutationCounter (source) Needs assignment
SingleBreakpointRecomb-2 Needs assignment
SingleBreakpointRecomb (source) Needs assignment
SiteRates (source) Needs assignment
SiteRates2 (source) Needs assignment
SlatkinMaddison-2parts Needs assignment
SlatkinMaddison (source) Needs assignment
SlidingNucWindow (source) Needs assignment
SlidingWindowAnalysis (source) Needs assignment
SplitSequencesByPattern (source) Needs assignment
SSRatesTest (source) Needs assignment
StarDecomposition (source) Needs assignment
StrandGRMTest (source) Needs assignment
StripStopCodons (source) Needs assignment
SubtreeSelectionComparison (source) Needs assignment
TestBranchDNDS (source) Needs assignment
TestClade (source) Needs assignment
TestCladeMeans (source) Needs assignment
TopologySearch (source) Needs assignment
TopologySearchConstrained (source) Needs assignment
TreeCorrelationCoefficients (source) Needs assignment
UpperBound (source) Needs assignment
NJ (source) Utility Needs assignment
PostScript (source) Utility Needs assignment
ProbabilityDistributions (source) Utility Needs assignment
PS_Plotters (source) Utility Needs assignment
ReadDelimitedFiles (source) Utility Needs assignment
TreeFunctions (source) Utility Needs assignment
WriteDelimitedFiles (source) Utility Needs assignment
WANC (source) Needs assignment
WebUpdate (source) Needs assignment
YangNielsenBranchSite2005 (source) Needs assignment
Filename Subfolder Filetype Brief description Comments Status


Include Files (*.ibf)

Filename Subfolder Brief description Comments Status
_BMS_Aux (source) Needs assignment
_CMS_Aux (source) Needs assignment
_MFReader_ (source) Needs assignment
_MSCOneStep (source) Needs assignment
_tipDater (source) Needs assignment
AddABias (source) Needs assignment
binomial (source) Needs assignment
dSdNTreeTools (source) Needs assignment
GA_CHC (source) Needs assignment
GA_CHC_Binary (source) Needs assignment
GA_CHC_kernel (source) Needs assignment
GADatedClock (source) Needs assignment
GARD_GA_CHC (source) Needs assignment
globalChecker (source) Needs assignment
Kernel_support (source) Needs assignment
ModelSelectorCodon (source) Needs assignment
pairwiseDistanceEstimator (source) Needs assignment
pairwiseDistanceEstimatorCounter (source) Needs assignment
partitionSequences (source) Needs assignment
qndhelper1 (source) Needs assignment
qndhelper1_mf (source) Needs assignment
qndhelper2 (source) Needs assignment
qndhelper2_mf (source) Needs assignment
qndhelper3 (source) Needs assignment
qndhelper4 (source) Needs assignment
lhc_supp (source) Samplers Needs assignment
srs (source) Samplers Needs assignment
SeqAlignmentCodonShared (source) Needs assignment
SeqAlignmentNucShared (source) Needs assignment
SeqAlignShared (source) Needs assignment
SequentialAddition (source) Needs assignment
GY94 (source) TemplateModels Needs assignment
HIVbetween (source) TemplateModels Needs assignment
HIVwithin (source) TemplateModels Needs assignment
MGFreqsEstimator (source) TemplateModels Needs assignment
MGwAA (source) TemplateModels Needs assignment
MGwEX (source) TemplateModels Needs assignment
TreeTools (source) Needs assignment
DBTools (source) Utility Needs assignment
Filename Subfolder Filetype Brief description Comments Status



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Database error - HyPhy Wiki

Database error

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A database query syntax error has occurred. This may indicate a bug in the software. The last attempted database query was:
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from within function "". Database returned error "5: database is locked".
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