Output files

This page lists all the output files of Agatta according to the command and optional flag to generate them.

The name of an output file is prefix.extension. The extension depends on the command (see table below) and reflects the content of the file. The prefix is by default agatta_out but can be changed by setting the prefix=filename flag.

Extension	Command	Content
.log	analysis	Log of the analysis.
.triplet and .taxabloc	analysis, tripdec	.triplet list of all triplets deduced from the input character trees. Each row corresponds to one triplet with its weight as a fraction and as a float. .taxabloc is a table file with the correspondance between leaf identifiers in .triplet and names given in the input.
.triplet_table.csv	tripdec --detailed_tripdec	Optional table with triplets generated by tripdec in rows and characters in columns. Each cell corresponds to the weight of the triplet extracted from the corresponding character. The last row and column sums all the weights.
.nex	analysis --software=paup	Triplet matrix in nexus format for three-item analysis by PAUP*.
.tnt	analysis --software=tnt, convert	Triplet matrix in nexus format for three-item analysis by TNT.
.tre	analysis, convert	Newick file recording all optimal rooted trees found during the analysis, with node support if option –support.
.tre	hmatrix	Newick list of rooted trees extracted from a hierarchical matrix.
.constrict	analysis --consensus=strict, consensus --consensus=strict	Newick file with the strict consensus.
.rcc	analysis --consensus=rcc, consensus --consensus=rcc	Newick file with the rcc profile comprising the strict consensus and eventually other informative subtrees.
.stand	analysis --rosetta, standardisation	List of standardised rooted trees in newick format. For biogeographic analyses, list of areagrams issued from a list of phylogenies where terminal taxa are replaced by areas.
.pdf	analysis --pdf, chartest	Mapping of character states on the cladogram. One pdf computed for each state.
.ri	analysis --ri	Retention index of the resulting cladogram plus a retention index for each character.
.itri	support --index=itri	ITRI between a reference tree and a reconstructed tree.
.dist	support --index=itrisym_sum, support --index=itrisym_product	Weighted triplet distance between two trees.
.chartest and chartest_node	analysis --chartest, chartest	The .chartest file gives all locations of the states on the cladogram and if the test is passed or not, sorted by state, and .chartest_node gives the same information sorted by node.
.poly	analysis, fp	List of duplication-free subtrees trees in newick format with their correspondance to their parent tree. Automatically generated within analysis if duplications are detected among the input trees.
.dt	describetree	List of basic informations about a list of rooted trees.