KITSCH
KITSCH. This program 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. . Part of Phylip.
© Copyright 1991-2006 by the University of Washington. Written by Joseph Felsenstein. Edited by NGBW team.
Manual: http://evolution.genetics.washington.edu/phylip/doc/kitsch.html
INPUT = DNA Distance matrix
TEST DATA SET
7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
TEST SET OUTPUT FILE (with all numerical options on)
7 Populations Fitch-Margoliash method with contemporary tips, version 3.66
__ __ 2
\ \ (Obs - Exp)
Sum of squares = /_ /_ ------------
2
i j Obs
negative branch lengths not allowed
Name Distance
---- ---------
Bovine 0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050
Mouse 1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290
Gibbon 1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830
Orang 1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100
Gorilla 1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830
Chimp 1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920
Human 1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000
+-------Human
+-6
+----5 +-------Chimp
! !
+---4 +---------Gorilla
! !
+------------------------3 +--------------Orang
! !
+----2 +------------------Gibbon
! !
--1 +-------------------------------------------Mouse
!
+------------------------------------------------Bovine
Sum of squares = 0.107
Average percent standard deviation = 5.16213
From To Length Height
---- -- ------ ------
6 Human 0.13460 0.81285
5 6 0.02836 0.67825
6 Chimp 0.13460 0.81285
4 5 0.07638 0.64990
5 Gorilla 0.16296 0.81285
3 4 0.06639 0.57352
4 Orang 0.23933 0.81285
2 3 0.42923 0.50713
3 Gibbon 0.30572 0.81285
1 2 0.07790 0.07790
2 Mouse 0.73495 0.81285
1 Bovine 0.81285 0.81285