Man pages for uqrmaie1/admixtools
Inferring demographic history from genetic data

admixtoolsTools for inferring demographic history from genetic data
afs_to_countsCompute count blocks and write them to disk
afs_to_f2Compute f2 blocks and write them to disk
afs_to_f2_blocksCompute all pairwise f2 statistics
agraph_to_igraphConvert agraph to igraph
boo_listGenerate a list of bootstrap resampled arrays
compare_fitsCompare the fit of two qpgraph models
compare_fits2Compare the fit of two qpgraph models
compare_fits4Compare the fit of two qpgraph models
count_snpsCount SNPs in an f2-statistics array
count_zero_edgesCount zero-length edges
decomposed_tree_neighborsFind all trees within SPR distance of 1 of all graph...
delete_admixDelete an admixture edge
delete_groupsDelete groups
delete_leafRemove population from graph
desimplify_graphAdd two nodes before each admixture node
edges_to_igraphConvert data frame graph to igraph
eigenstrat_to_afsRead allele frequencies from _EIGENSTRAT_ files
est_to_booTurn per-block estimates into bootstrap estimates
est_to_looTurn per-block estimates into leave-one-out estimates
example_annoData frame with sample annotations
example_f2_blocksBlocked f2-statistics for 7 populations
example_graphAdmixture graph for 7 populations
example_igraphAdmixture graph for 7 populations
example_optData frame with one fitted admixture graph
example_qpgraph_ref_resultsexample_graph fitted using qpGraph
example_triplesData frame with population triples
extract_afsCompute and store blocked allele frequency data
extract_afs_simpleCompute and store blocked allele frequency data
extract_countsExtract and store data needed to compute blocked f2
extract_f2Compute and store blocked f2 statistics
extract_f2_largeCompute and store blocked f2 statistics
extract_f2_subsetCopy f2-statistics
extract_samplesExtract samples from PLINK files
f2Estimate f2 statistics
f2dat_f4datTurn f2 data to f4 data
f2_from_genoCompute blocked f2 statistics
f2_from_msprimeSimulate an admixture graph in msprime
f2_from_precompRead blocked f2 statistics from disk
f3blockdat_from_genof3 from genotype data
f4blockdat_from_genof4 from genotype data
f4blockdat_to_f4blocksTurn f4 block data to 3d array
f4_from_afdatCompute f4 from allele frequencies
f4_from_f2Get per-block f4-statistics
find_admixedgesFind admixture edges
find_graphsFind well fitting admixture graphs
find_graphs_oldFind well fitting admixture graphs
find_newedgesFind possible new edges
find_normedgesFind drift edges
flipadmix_randomModify a graph flipping the direction of an admixture edge
fstCompute Fst
generate_all_graphsGenerate all graphs
generate_all_treesGenerate all trees
get_block_lengthsFind LD-independent blocks
get_f2Turns f2_data into f2_blocks
get_leafnamesGet the population names of a graph
get_outpopGet the outgroup from a graph (if it exists)
get_rootnameGet the root name
graph_addleafAdd a population to an admixture graph
graph_distancesPairwise distance estimates for graphs
graph_equationsFind well fitting admixture graphs
graph_f2_functionMake a function representing a graph
graph_flipadmixFind all valid graphs which result from flipping one...
graph_hashGet unique hash of an admixture graph
graph_minusoneFind all graphs which result from removing one admixture edge
graph_minusplusFind all graphs which result from adding and removing one...
graphmod_pavelReturn all graphs created from permuting a subclade
graph_plusoneFind all graphs which result from adding one admixture edge
graph_splittreesFind all trees which are part of the admixture graph
graph_to_afsSimulate allele frequncies under an admixture graph
graph_to_pcsSimulate PCs under an admixture graph
graph_to_qpadmGet all qpadm models for a graph
group_samplesGroup precomputed data
igraph_to_agraphConvert igraph to agraph
insert_admixInsert a single edge into graph
insert_admix_nInsert admixture edges into graph
insert_admix_oldInsert admixture edges into graph
insert_leafAdd population to graph
isomorphism_classesFind identical graphs
isomorphism_classes2Find identical graphs
is_validTest if an admixture graph is valid
joint_sfsJoint site frequency spectrum
joint_spectrumEstimate joint allele frequency spectrum
lazadmEstimate admixture weights
loo_listGenerate a list of leave-one-out arrays
loo_to_estTurn leave-one-out estimates to per-block estimates
move_admixedge_onceModify a graph by moving an admixture edge
msprime_genomeSimulate an admixture graph in msprime v1.x.
msprime_simSimulate an admixture graph in msprime v1.x
mutate_nModify a graph by applying n mutation functions
newick_to_edgesTurn a newick format tree to a matrix of edges
node_countsCount how often each node in graph occurs in other graphs
node_signatureReturns a signature of a graph consisting of the left and...
numadmixCount number of admixture nodes
packedancestrymap_to_afsRead allele frequencies from packedancestrymap files
packedancestrymap_to_plinkConvert _EIGENSTRAT_ or _PACKEDANCESTRYMAP_ to _PLINK_
parse_dotRead graph in dot format
parse_qp3pop_outputRead qp3Pop output file
parse_qpadm_outputRead qpAdm output file
parse_qpdstat_outputRead qpDstat output file
parse_qpf4ratio_outputRead qpF4ratio output file
parse_qpgraph_graphfileRead qpGraph graph file
parse_qpgraph_outputRead qpGraph output file
permute_leavesModify a graph by permuting leaf nodes
place_root_randomModify a graph by changing the position of the root node
plink_to_afsRead allele frequencies from 'PLINK' files
plot_comparisonCompare two models
plot_graphPlot an admixture graph
plot_graph_mapPlot an admixture graph on a map
plotly_comparisonCompare two models
plotly_graphPlot an admixture graph using plotly
plot_mapPlot samples on a map
pseudo_datesGet pseudo dates for graph nodes
qp3popEstimate f3 statistics
qp3pop_wrapperWrapper function around the original qp3Pop program
qpadmEstimate admixture weights
qpadm_modelsPartition a list of populations into left and right...
qpadm_models_oldReturn all valid qpAdm models for an admixturegraph
qpadm_multiRun multiple qpadm models
qpadm_pFaster version of 'qpadm' with reduced output
qpadm_rotateCompute p-values for many qpadm models
qpadm_wrapperWrapper function around the original qpAdm program
qpdstatEstimate f4 statistics
qpdstat_wrapperWrapper function around the original qpDstat program
qpf4diffEstimate f4 differences
qpf4ratioEstimate admixture proportions via f4 ratios
qpf4ratio_wrapperWrapper function around the original qpF4ratio program
qpfstatsGet smoothed f2-statistics
qpgraphCompute the fit of an admixture graph
qpgraph_precompute_f3Compute f3-statistics from f2-statistics.
qpgraph_resample_multiEvaluate a qpgraph models many times
qpgraph_resample_snps2Evaluate a qpgraph model many times
qpgraph_wrapperWrapper function around the original qpGraph program
qpwaveEstimate admixture waves
qpwave_pairsCompute all pairwise qpwave p-values
qpwave_wrapperWrapper function around the original qpWave program
random_admixturegraphGenerate a random admixture graph
random_datesGet random dates for graph nodes
random_newickGenerate a random binary graph
random_simGenerate a random graph and simulate it in msprime v1.x
read_eigenstratRead genotype data from _EIGENSTRAT_ files
read_f2Read blocked f2 estimates from disk
read_packedancestrymapRead genotype data from packedancestrymap files
read_plinkRead genotype data from 'PLINK' files
resample_indsRun models while leaving out individuals
resample_snpsRun models while leaving out SNP blocks
rotate_modelsRotate populations between left and right
run_shiny_admixtoolsLaunch ADMIXTOOLS 2 GUI
satisfies_constraintsTest constraints on a graph
satisfies_eventorderTest f4 constraints on a graph
satisfies_nonzerof4Test f4 constraints on a graph
satisfies_numadmixTest admixture constraints on a graph
satisfies_zerof4Test f4 constraints on a graph
shortest_unique_prefixesReturn shortest unique prefixes
simplify_graphRemove redundant edges
split_matSplit a matrix into blocks
split_multifurcationsSplit nodes with more than two edges
spr_allModify a graph by regrafting a subcomponent
spr_leavesModify a graph by regrafting a leaf
summarize_descendantsList leaf nodes for all internal nodes
summarize_descendants_listList leaf nodes for all internal nodes in a list of graphs
summarize_eventorderList population split events in a graph
summarize_eventorder_listList population split events in a list of graphs
summarize_fitsSummarize graph fits
summarize_numadmixList number of admixture events for each population
summarize_numadmix_listList number of admixture events for each population in a list...
summarize_proxiesAssign proxy populations to admixed populations
summarize_proxies_listList proxy populations in graphlist
summarize_triplesSummarize triples across graphs
summarize_zerof4List clades in a graph
summarize_zerof4_listList clades in a list of graphs
swap_leavesModify a graph by swapping two leaf nodes
test_cladalityTest if two sets of populations form two clades
tree_in_graphTest if a tree is part of a graph
tree_neighborsFind all trees within SPR distance of 1
unidentifiable_edgesFind all unidentifiable edges
write_dotConvert graph to dot format
write_f2Write blocked f2 estimates to disk
uqrmaie1/admixtools documentation built on March 4, 2024, 10:19 p.m.