hivtree                 package:ape                 R Documentation

_P_h_y_l_o_g_e_n_e_t_i_c _T_r_e_e _o_f _1_9_3 _H_I_V-_1 _S_e_q_u_e_n_c_e_s

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

     This data set describes an estimated clock-like phylogeny of 193
     HIV-1 group M sequences sampled in the Democratic Republic of
     Congo.

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

     data(hivtree.newick)
     data(hivtree.table)

_F_o_r_m_a_t:

     'hivtree.newick' is a string with the tree in Newick format. The
     data frame 'hivtree.table' contains the corresponding internode
     distances.

_S_o_u_r_c_e:

     This is a data example from Strimmer and Pybus (2001).

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

     Strimmer, K. and Pybus, O. G. (2001) Exploring the demographic
     history of DNA sequences using the generalized skyline plot.
     _Molecular Biology and Evolution_, *18*, 2298-2305.

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

     library(ape)

     # example tree in NH format (a string)
     data("hivtree.newick") 
     hivtree.newick

     # generate file "hivtree.phy" in working directory
     cat(hivtree.newick, file = "hivtree.phy", sep = "\n")
     tree.hiv <- read.tree("hivtree.phy") # load tree
     unlink("hivtree.phy") # delete the file "hivtree.phy"

     plot(tree.hiv)

     # table with list of internode distances
     data("hivtree.table") 
     hivtree.table

     # construct coalescence intervals
     ci <- coalescent.intervals(tree.hiv) # from tree
     ci <- coalescent.intervals(hivtree.table$size) #from intervals
     ci

