{
"result": "Neighbor -- Neighbor-Joining and UPGMA methods\n==============================================\n\n**Neighbor** implements the Neighbor-Joining method of Saitou and Nei (1987) and the UPGMA method of clustering.\n\nNeighbor constructs a tree by successive clustering of lineages, setting branch lengths as the lineages join. The tree is not rearranged thereafter. The tree does not assume an evolutionary clock, so that it is in effect an unrooted tree. It should be somewhat similar to the tree obtained by Fitch. The program cannot evaluate a User tree, nor can it prevent branch lengths from becoming negative. However the algorithm is far faster than Fitch or Kitsch. This will make it particularly effective in their place for large studies or for bootstrap or jackknife resampling studies which require runs on multiple data sets.\n\nThe UPGMA option constructs a tree by successive (agglomerative) clustering using an average-linkage method of clustering. It has some relationship to Kitsch, in that when the tree topology turns out the same, the branch lengths with UPGMA will turn out to be the same as with the P = 0 option of Kitsch. \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 : Choose between the Neighbor-Joining and UPGMA methods\n\n* Out Group Root : Specifies the number of the outgroup (the species being taken in the numerical order that they occur in the input file). Example : 6 means the sixth species in the data is taken as the outgroup. Outgroup-rooting will not be attempted if the data have already established a root for the tree from some other consideration, and may not be if it is a user-defined tree, despite your invoking the option.\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 tree (rooted if UPGMA, unrooted if Neighbor-Joining) and the lengths of the interior segments. The Average Percent Standard Deviation is not computed or printed out. If the tree found by Neighbor is fed into Fitch as a User Tree, it will compute this quantity if one also selects the N option of Fitch to ensure that none of the branch lengths is re-estimated.\nAs Neighbor runs it prints out an account of the successive clustering levels.\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\nNeighbor - 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.\n\nhttp://evolution.genetics.washington.edu/phylip/doc/neighbor.html\n\nContact\n-------\nProf. R. Sowdhamini(mini@ncbs.res.in) \nOommen K. Mathew (oommenkm@ncbs.res.in) \nMurugavel P\n"
}