# list of files and directories in the project
# (all *_rresults.txt are the output of Rresults script and not listed below)
000todo	TODO list
03_checks.r	separate R script to check tables
04_duplicated_ids_check.r	separate R script to check for duplicated IDs
13_make_wanted.r	R script which outputs names of non-sequenced species and other info
13_wanted/	directory to where "13_make_wanted.r" outputs results
20_make_sets.r	R script which collect DNA data into the "sets" (one per marker) for subsequent alignment
20_sets/	find sets here
30_align.r	R script which calls the chosen external alignment tool
30_alignments/	find alignments here
31_trim.r	R script which trim flanks of alignments
31_alignments_trimmed/	trimmed alignments here
32_gapcode.r	R script which call Gap.code() function to encode gaps
32_alignments_trimmed_gapcoded/	gapcoded alignments here
40_concatenate_and_stat.r	R script which concatenate sequences from one sample ("strict") and from different samples of one species ("semistrict"), and also outputs some statistics
40_concatenated/	directory where concatenated matrices ("super-matrices") and other "intermediate sources" are kept
50_technical_trees/	directory with output "techical" trees (single marker trees, k-mer trees from raw data and from semistrict super-matrix)
51_make_r_raw_kmer_trees.r	R script to build raw k-mer trees, with all data and with selected sequences only
52_make_r_semistrict_kmer_tree.r	R script to build k-mer trees on semistrict super-matrix
53_make_r_nj_single_marker_trees.r	R script to build NJ single marker trees
61_make_r_mp_semistrict_tree.r	R script to build MP (maximum parsimony) trees
70_raxml_working/	files from external RAxML tool
71_make_r_ml_modeltest.r	R script for maximal likelihood model testing
72_make_r_ml_trees.r	R script to estimate maximal likelihood trees
73_make_raxml_trees.r	R script to estimate maximal likelihood trees with erxternal RAxML tool
80_mrbayes_working/	files from external MrBayes tool
81_make_mrbayes_semistrict_tree.r	R script to estimate Bayesian trees with external MrBayes tool
99_trees/	resulted trees in PDF and also in Newick format
_kubricks_dna.txt	local DNA database
_kubricks_dna_c.txt	explanation of variables in the "dna" table
_kubricks_sp.txt	taxonomical data
_kubricks_sp_c.txt	explanation of variables in the "sp" table
_kubricks_treesp.txt	analysis-specific species labels
_kubricks_treesp_c.txt	explanation of variables in the "treesp" table
make_all	shell script to run the whole pipeline
make_check	shell script to check if runs went without errors
make_data	shell script to make alignments and concatenated matrix
make_gzip	shell script to pack results of MrBayes run (otherwise, files are very big)
make_model_test	shell script to run model testing
make_technical_trees	shell script to build technical trees (see above)
make_trees_semistrict	shell script to make resulted trees
README	description of the package and installation instructions
README_files	this file