构建系统发育树需要注意的几个问题

按路径输入刚才生成的 *.PHY文件，显示如下： Bootstrapping algorithm, version 3.6a3 Settings for this run:

D Sequence, Morph, Rest., Gene Freqs? Molecular sequences J Bootstrap, Jackknife, Permute, Rewrite? Bootstrap B Block size for block-bootstrapping? 1 R How many replicates? 100 W Read weights of characters? No C Read categories of sites? No

F Write out data sets or just weights? Data sets I Input sequences interleaved? Yes 0 Terminal type none 1 Print out the data at start of run No 2 Print indications of progress of run Yes Y to accept these of type the letter for one to change R

Number of replicates? 1000 0

Settings for this run:

D Sequence, Morph, Rest., Gene Freqs? Molecular sequences J Bootstrap, Jackknife, Permute, Rewrite? Bootstrap B Block size for block-bootstrapping? 1 R How many replicates? 1000 W Read weights of characters? No C Read categories of sites? No

F Write out data sets or just weights? Data sets I Input sequences interleaved? Yes

0 Terminal type IBM PC 1 Print out the data at start of run No

2 Print indications of progress of run Yes Y to accept these of type the letter for one to change Y

Random number seed (must be odd)? 5(any odd number)

completed replicate number 100 completed replicate number 200 completed replicate number 300 completed replicate number 400 completed replicate number 500 completed replicate number 600 completed replicate number 700 completed replicate number 800 completed replicate number 900 completed replicate number 1000

上面的D、J、R、I、O、1、2代表可选择的选项，键入这些字母后敲回车键，程序的条件就会发生改变。D选项无须改变。J选项有三种条件可以选择，分别是Bootstrap、Jackknife和Permute。R选项让使用者输入republicate的数目。所谓republicate就是用Bootstrap法生成的一个多序列组。根据多序列中所含的序列的数目的不同可以选取不同的republicate。当我们设置好条件后，键入Y按回车。得到一个文件outfile：C:\\Program Files\\Phylip\\exe\\ outfile. 重命名outfile→infile。 (2) 打开dnadist.exe

Nucleic acid sequence Distance Matrix program, version 3.6a3 Settings for this run:

D Distance ? F84 G Gamma distributed rates across sites? No T Transition/transversion ratio? 2.0 C One category of substitution rates? Yes W Use weights for sites? No

F Use emperical base frequencies? Yes L Form of distance matrix? Square M Analyze multiple data sets? No I Input sequences interleaved? Yes

0 Terminal type ? 1 Print out the data at start of run No 2 Print indications of progress of run Yes Y to accept these of type the letter for one to change d

D Distance ? Kimura 2-parameter m

Multiple data sets or multiple weighs? (type D or W) d

How many data sets? 1000 0

Settings for this run:

D Distance ? Kimura 2-parameter G Gamma distributed rates across sites? No T Transition/transversion ratio? 2.0 C One category of substitution rates? Yes W Use weights for sites? No

F Use emperical base frequencies? Yes L Form of distance matrix? Square

M Analyze multiple data sets? Yes, 1000 data sets I Input sequences interleaved? Yes

0 Terminal type ? IBM PC 1 Print out the data at start of run No 2 Print indications of progress of run Yes

Y to accept these of type the letter for one to change

Y

选项D有四种距离模式可以选择，分别是Kimura 2-parameter、Jin/Nei、Maximum-likelihood和Jukes-Cantor。选项T一般键入一个1.5-3.0之间的数字。选项M键入1000。运行后生成文件C:\\Program Files\\Phylip\\exe\\ outfile。 重命名outfile→infile。 (3) 打开 neighbor.exe

Neighbor-Joining/UPGMA method version 3.6a3 Settings for this run:

N Neighbor-Joining or UPGMA tree? Neighbor-Joining O Outgroup root? No, Use as outgroup species 1 L Lower-triangular data metrix? No R Upper-triangular data metrix? No S Subreplication? No

J Randomize input order of species? No, Use input order M Analyze multiple data sets? No

0 Terminal type ? 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes

4 Write out trees onto tree file? Yes

Y to accept these of type the letter for one to change m

How many data sets? 1000

Random number seed (must be odd)? 5

Settings for this run:

N Neighbor-Joining or UPGMA tree? Neighbor-Joining O Outgroup root? No, Use as outgroup species 1 L Lower-triangular data metrix? No