{
"result": "Kitsch -- Fitch-Margoliash and Least Squares Methods with Evolutionary Clock\n=====================================================================\n\n**Kitsch** carries out the Fitch-Margoliash and Least Squares methods, plus a variety of others of the same family, with the assumption that all tip species are contemporaneous, and that there is an evolutionary clock (in effect, a molecular clock). This means that branches of the tree cannot be of arbitrary length, but are constrained so that the total length from the root of the tree to any species is the same. The quantity minimized is the same weighted sum of squares described in the Distance Matrix Methods documentation file.\n\nInput Files\n-----------\n* **Sequence Text** : The input format is same as documented in Distance Matrix Methods documentation file (http://evolution.genetics.washington.edu/phylip/doc/distance.html). The first line of the input file contains the number of species. There follows species data, starting, as with all other programs, with a species name. The species name is ten characters long, and must be padded out with blanks if shorter. For each species there then follows a set of distances to all the other species (options selected in the programs' menus allow the distance matrix to be upper or lower triangular or square). The distances can continue to a new line after any of them. If the matrix is lower-triangular, the diagonal entries (the distances from a species to itself) will not be read by the programs. \n **OR** \n* **Sequence File** : Path to a file containing the above text\n \nParameters\n----------\n* Method : This option allows choice between the Fitch-Margoliash criterion and the Minimum Evolution method . Minimum Evolution uses the Fitch-Margoliash criterion to fit branch lengths to each topology, but then chooses topologies based on their total branch length. There is no constraint on negative branch lengths in the Minimum Evolution method; it sometimes gives rather strange results, as it can like solutions that have large negative branch lengths, as these reduce the total sum of branch lengths! \n\n* Power : choose the power (P) at a value that results in the standard deviation of the variation of the observed from the expected distances being the P/2-th power of the expected distance.\n\n* Lower-Triangular DataMatrix,Upper-Triangular DataMatrix : The choice\nallows the distance matrix to be upper or lower triangular or square\n\n* SubReplicates : Choose to turn on subreplication option\n\nDisplayed Results\n------------------\nTwo tabs Results and Out-Tree are displayed\n\n* Result is a rooted tree, together with the sum of squares, the number of tree topologies searched, and, if the power P is at its default value of 2.0, the Average Percent Standard Deviation is also supplied. The lengths of the branches of the tree are given in a table, that also shows for each branch the time at the upper end of the branch. \"Time\" here really means cumulative branch length from the root, going upwards (on the printed diagram, rightwards). For each branch, the \"time\" given is for the node at the right (upper) end of the branch. It is important to realize that the branch lengths are not exactly proportional to the lengths drawn on the printed tree diagram! In particular, short branches are exaggerated in the length on that diagram so that they are more visible. \n\n\n* Out Tree gives the final tree in newick format\n \nDownloadable Results\n--------------------\n\n* Results: File containing the displayed result\n\n* OutTree : final tree in newick format\n\n* Log File: Execution log \n\n\nKitsch - Reference\n-------------------\nFelsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.\nFelsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.\nhttp://evolution.genetics.washington.edu/phylip/doc/kitsch.html\n\nContact\n-------\nProf. R. Sowdhamini(mini@ncbs.res.in) \nOommen K. Mathew (oommenkm@ncbs.res.in) \nMurugavel P\n"
}