klastorin                package:ape                R Documentation

_K_l_a_s_t_o_r_i_n'_s (_1_9_8_2) _m_e_t_h_o_d _f_o_r _c_l_a_s_s_i_f_y_i_n_g _g_e_n_e_s _a_s _s_u_g_g_e_s_t_e_d _b_y _M_i_s_a_w_a
_a_n_d _T_a_j_i_m_a (_2_0_0_0)

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'klastorin' uses the method by Klastorin's (1982) as
     suggested by Misawa and Tajima (2000) for identifying groups
     within gene trees.

_U_s_a_g_e:

     klastorin(phy)

_A_r_g_u_m_e_n_t_s:

     phy: a phylogenetic tree, i.e. an object of class '"phy"'. The
          root of the tree should make sense biologically. 

_V_a_l_u_e:

     A vector indication the class affiliation for each sequence/taxon
     in the tree.

_A_u_t_h_o_r(_s):

     Gangolf Jobb (<URL: http://www.treefinder.de>)

_R_e_f_e_r_e_n_c_e_s:

     Klastorin T.D. (1982) An alternative method for hospital partition
     determination using hierarchical cluster analysis. _Operations
     Research_ *30*,1134-1147.

     Misawa, K. (2000) A simple method for classifying genes and a
     bootstrap test for classifications. _Molecular Biology and
     Evolution_, *17*, 1879-1884.

_S_e_e _A_l_s_o:

     'opsin'.

_E_x_a_m_p_l_e_s:

     library(ape)

     # find groups in landplant tree 
     data("landplants.newick") 
     tree1 <- read.tree(text = landplants.newick)
     plot(tree1, label.offset = 0.001)
     klastorin(tree1) 
     tree1$tip.label

     # find groups in opsin tree 
     data("opsin.newick") 
     tree2 <- read.tree(text = opsin.newick)
     plot(tree2,label.offset = 0.01)
     groups <- klastorin(tree2) 
     groups
     tree2$tip.label[groups==1]
     tree2$tip.label[groups==2]
     tree2$tip.label[groups==3]
     tree2$tip.label[groups==4]
     tree2$tip.label[groups==5]

