Man pages for uqrmaie1/admixtools
Inferring demographic history from genetic data
| admixtools | Tools for inferring demographic history from genetic data |
| afs_to_counts | Compute count blocks and write them to disk |
| afs_to_f2 | Compute f2 blocks and write them to disk |
| afs_to_f2_blocks | Compute all pairwise f2 statistics |
| agraph_to_igraph | Convert agraph to igraph |
| boo_list | Generate a list of bootstrap resampled arrays |
| compare_fits | Compare the fit of two qpgraph models |
| compare_fits2 | Compare the fit of two qpgraph models |
| compare_fits4 | Compare the fit of two qpgraph models |
| count_snps | Count SNPs in an f2-statistics array |
| count_zero_edges | Count zero-length edges |
| decomposed_tree_neighbors | Find all trees within SPR distance of 1 of all graph... |
| delete_admix | Delete an admixture edge |
| delete_groups | Delete groups |
| delete_leaf | Remove population from graph |
| desimplify_graph | Add two nodes before each admixture node |
| edges_to_igraph | Convert data frame graph to igraph |
| eigenstrat_to_afs | Read allele frequencies from _EIGENSTRAT_ files |
| est_to_boo | Turn per-block estimates into bootstrap estimates |
| est_to_loo | Turn per-block estimates into leave-one-out estimates |
| example_anno | Data frame with sample annotations |
| example_f2_blocks | Blocked f2-statistics for 7 populations |
| example_graph | Admixture graph for 7 populations |
| example_igraph | Admixture graph for 7 populations |
| example_opt | Data frame with one fitted admixture graph |
| example_qpgraph_ref_results | example_graph fitted using qpGraph |
| example_triples | Data frame with population triples |
| extract_afs | Compute and store blocked allele frequency data |
| extract_afs_simple | Compute and store blocked allele frequency data |
| extract_counts | Extract and store data needed to compute blocked f2 |
| extract_f2 | Compute and store blocked f2 statistics |
| extract_f2_large | Compute and store blocked f2 statistics |
| extract_f2_subset | Copy f2-statistics |
| extract_samples | Extract samples from PLINK files |
| f2 | Estimate f2 statistics |
| f2dat_f4dat | Turn f2 data to f4 data |
| f2_from_geno | Compute blocked f2 statistics |
| f2_from_msprime | Simulate an admixture graph in msprime |
| f2_from_precomp | Read blocked f2 statistics from disk |
| f3blockdat_from_geno | f3 from genotype data |
| f4blockdat_from_geno | f4 from genotype data |
| f4blockdat_to_f4blocks | Turn f4 block data to 3d array |
| f4_from_afdat | Compute f4 from allele frequencies |
| f4_from_f2 | Get per-block f4-statistics |
| find_admixedges | Find admixture edges |
| find_graphs | Find well fitting admixture graphs |
| find_graphs_old | Find well fitting admixture graphs |
| find_newedges | Find possible new edges |
| find_normedges | Find drift edges |
| flipadmix_random | Modify a graph flipping the direction of an admixture edge |
| fst | Compute Fst |
| generate_all_graphs | Generate all graphs |
| generate_all_trees | Generate all trees |
| get_block_lengths | Find LD-independent blocks |
| get_f2 | Turns f2_data into f2_blocks |
| get_leafnames | Get the population names of a graph |
| get_outpop | Get the outgroup from a graph (if it exists) |
| get_rootname | Get the root name |
| graph_addleaf | Add a population to an admixture graph |
| graph_distances | Pairwise distance estimates for graphs |
| graph_equations | Find well fitting admixture graphs |
| graph_f2_function | Make a function representing a graph |
| graph_flipadmix | Find all valid graphs which result from flipping one... |
| graph_hash | Get unique hash of an admixture graph |
| graph_minusone | Find all graphs which result from removing one admixture edge |
| graph_minusplus | Find all graphs which result from adding and removing one... |
| graphmod_pavel | Return all graphs created from permuting a subclade |
| graph_plusone | Find all graphs which result from adding one admixture edge |
| graph_splittrees | Find all trees which are part of the admixture graph |
| graph_to_afs | Simulate allele frequncies under an admixture graph |
| graph_to_pcs | Simulate PCs under an admixture graph |
| graph_to_qpadm | Get all qpadm models for a graph |
| group_samples | Group precomputed data |
| igraph_to_agraph | Convert igraph to agraph |
| insert_admix | Insert a single edge into graph |
| insert_admix_n | Insert admixture edges into graph |
| insert_admix_old | Insert admixture edges into graph |
| insert_leaf | Add population to graph |
| isomorphism_classes | Find identical graphs |
| isomorphism_classes2 | Find identical graphs |
| is_valid | Test if an admixture graph is valid |
| joint_sfs | Joint site frequency spectrum |
| joint_spectrum | Estimate joint allele frequency spectrum |
| lazadm | Estimate admixture weights |
| loo_list | Generate a list of leave-one-out arrays |
| loo_to_est | Turn leave-one-out estimates to per-block estimates |
| move_admixedge_once | Modify a graph by moving an admixture edge |
| msprime_genome | Simulate an admixture graph in msprime v1.x. |
| msprime_sim | Simulate an admixture graph in msprime v1.x |
| mutate_n | Modify a graph by applying n mutation functions |
| newick_to_edges | Turn a newick format tree to a matrix of edges |
| node_counts | Count how often each node in graph occurs in other graphs |
| node_signature | Returns a signature of a graph consisting of the left and... |
| numadmix | Count number of admixture nodes |
| packedancestrymap_to_afs | Read allele frequencies from packedancestrymap files |
| packedancestrymap_to_plink | Convert _EIGENSTRAT_ or _PACKEDANCESTRYMAP_ to _PLINK_ |
| parse_dot | Read graph in dot format |
| parse_qp3pop_output | Read qp3Pop output file |
| parse_qpadm_output | Read qpAdm output file |
| parse_qpdstat_output | Read qpDstat output file |
| parse_qpf4ratio_output | Read qpF4ratio output file |
| parse_qpgraph_graphfile | Read qpGraph graph file |
| parse_qpgraph_output | Read qpGraph output file |
| permute_leaves | Modify a graph by permuting leaf nodes |
| place_root_random | Modify a graph by changing the position of the root node |
| plink_to_afs | Read allele frequencies from 'PLINK' files |
| plot_comparison | Compare two models |
| plot_graph | Plot an admixture graph |
| plot_graph_map | Plot an admixture graph on a map |
| plotly_comparison | Compare two models |
| plotly_graph | Plot an admixture graph using plotly |
| plot_map | Plot samples on a map |
| pseudo_dates | Get pseudo dates for graph nodes |
| qp3pop | Estimate f3 statistics |
| qp3pop_wrapper | Wrapper function around the original qp3Pop program |
| qpadm | Estimate admixture weights |
| qpadm_models | Partition a list of populations into left and right... |
| qpadm_models_old | Return all valid qpAdm models for an admixturegraph |
| qpadm_multi | Run multiple qpadm models |
| qpadm_p | Faster version of 'qpadm' with reduced output |
| qpadm_rotate | Compute p-values for many qpadm models |
| qpadm_wrapper | Wrapper function around the original qpAdm program |
| qpdstat | Estimate f4 statistics |
| qpdstat_wrapper | Wrapper function around the original qpDstat program |
| qpf4diff | Estimate f4 differences |
| qpf4ratio | Estimate admixture proportions via f4 ratios |
| qpf4ratio_wrapper | Wrapper function around the original qpF4ratio program |
| qpfstats | Get smoothed f2-statistics |
| qpgraph | Compute the fit of an admixture graph |
| qpgraph_precompute_f3 | Compute f3-statistics from f2-statistics. |
| qpgraph_resample_multi | Evaluate a qpgraph models many times |
| qpgraph_resample_snps2 | Evaluate a qpgraph model many times |
| qpgraph_wrapper | Wrapper function around the original qpGraph program |
| qpwave | Estimate admixture waves |
| qpwave_pairs | Compute all pairwise qpwave p-values |
| random_admixturegraph | Generate a random admixture graph |
| random_dates | Get random dates for graph nodes |
| random_newick | Generate a random binary graph |
| random_sim | Generate a random graph and simulate it in msprime v1.x |
| read_eigenstrat | Read genotype data from _EIGENSTRAT_ files |
| read_f2 | Read blocked f2 estimates from disk |
| read_packedancestrymap | Read genotype data from packedancestrymap files |
| read_plink | Read genotype data from 'PLINK' files |
| resample_inds | Run models while leaving out individuals |
| resample_snps | Run models while leaving out SNP blocks |
| rotate_models | Rotate populations between left and right |
| run_shiny_admixtools | Launch ADMIXTOOLS 2 GUI |
| satisfies_constraints | Test constraints on a graph |
| satisfies_eventorder | Test f4 constraints on a graph |
| satisfies_nonzerof4 | Test f4 constraints on a graph |
| satisfies_numadmix | Test admixture constraints on a graph |
| satisfies_zerof4 | Test f4 constraints on a graph |
| shortest_unique_prefixes | Return shortest unique prefixes |
| simplify_graph | Remove redundant edges |
| split_mat | Split a matrix into blocks |
| split_multifurcations | Split nodes with more than two edges |
| spr_all | Modify a graph by regrafting a subcomponent |
| spr_leaves | Modify a graph by regrafting a leaf |
| summarize_descendants | List leaf nodes for all internal nodes |
| summarize_descendants_list | List leaf nodes for all internal nodes in a list of graphs |
| summarize_eventorder | List population split events in a graph |
| summarize_eventorder_list | List population split events in a list of graphs |
| summarize_fits | Summarize graph fits |
| summarize_numadmix | List number of admixture events for each population |
| summarize_numadmix_list | List number of admixture events for each population in a list... |
| summarize_proxies | Assign proxy populations to admixed populations |
| summarize_proxies_list | List proxy populations in graphlist |
| summarize_triples | Summarize triples across graphs |
| summarize_zerof4 | List clades in a graph |
| summarize_zerof4_list | List clades in a list of graphs |
| swap_leaves | Modify a graph by swapping two leaf nodes |
| test_cladality | Test if two sets of populations form two clades |
| tree_in_graph | Test if a tree is part of a graph |
| tree_neighbors | Find all trees within SPR distance of 1 |
| unidentifiable_edges | Find all unidentifiable edges |
| write_dot | Convert graph to dot format |
| write_f2 | Write blocked f2 estimates to disk |
