通過PAML中的CODEML模組計算dnds的過程以及踩坑

chestnut_egg發表於2020-05-15

最近幫女朋友做畢業設計的時候用到了 PAML這個軟體的codeml功能，發現網上相關的資料很少，於是把自己踩的一些坑分享一下，希望能幫到其他有相同困難的人

 

一、下載與安裝

PAML軟體下載地址

http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz

DAMBE軟體下載地址

http://dambe.bio.uottawa.ca/DAMBE/dambe_install_win.aspx

 

二、使用方法

首先準備好你的fas檔案

我們需要將fas檔案轉換一下格式，方法很多，我這邊說兩種方法，這兩種方法最後得到的檔案內容完全相同，只是字尾名不同

 

方法一：

使用python指令碼轉換

將你的*.fas檔案與指令碼放在同一目錄下，執行指令碼，會生成一個.phy檔案

import re
with open('seven.fas', 'r') as fin:
    sequences = [(m.group(1), ''.join(m.group(2).split()))
                 for m in re.finditer(r'(?m)^>([^ \n]+)[^\n]*([^>]*)', fin.read())]
with open('seven.phy', 'w') as fout:
    fout.write('%d %d\n' % (len(sequences), len(sequences[0][1])))
    for item in sequences:
        fout.write('%-20s %s\n' % item)

 

方法二：

使用DAMBE軟體轉換格式

1.開啟DAMBE，選擇 File -> Open standard sequence file -> 檔案型別選擇為包含 fas 型別 -> 選擇你的fas檔案

 

 

 2.點選 go

 

 

 3.點選 File -> save or convert sequence format  -> 選擇 paml 格式

 

 

 4.手動修改 *.pml 的字尾名為 *.nuc

 

 

 

 

通過以上兩個方法會得到一份 *.phy 或者 *.nuc 檔案

接下來需要去除序列中的終止密碼子 

 TAG,TAA,TGA

你可以全選檔案內容查詢替換 將  TAG/TAA/TGA 替換為 ---

也可以使用下面這個python指令碼

import re

with open(r'seven.phy', 'r') as f:
    content = f.read()
    content = content.replace("TAG","---")
    content = content.replace("TAA", "---")
    content = content.replace("TGA", "---")
    # print(content)

with open('sevenend.phy', 'w') as f:
    f.write(content)

會生成一個去除過終止密碼子的檔案

 

現在將這個處理過後的序列檔案*.phy與樹檔案、配置檔案codeml.ctl三個放在  \paml4.9j\bin 目錄下

配置檔案codeml.ctl內容如下可參考 一般修改前面三行即可 按順序為序列檔名 樹檔名 輸出檔名

      seqfile = seven.nuc * sequence data filename
     treefile = Newick      * tree structure file name
      outfile = test.txt           * main result file name

        noisy = 0  * 0,1,2,3,9: how much rubbish on the screen
      verbose = 0  * 0: concise; 1: detailed, 2: too much
      runmode = -2  * 0: user tree;  1: semi-automatic;  2: automatic
                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

*        ndata = 5504
        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

        model = 0
                   * models for codons:
                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
                   * models for AAs or codon-translated AAs:
                       * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                       * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

      NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                   * 13:3normal>0

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
        Mgene = 0
                   * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
                   * AA: 0:rates, 1:separate

    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
        kappa = 2  * initial or fixed kappa
    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
        omega = .4 * initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
        alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0  * different alphas for genes
        ncatG = 8  * # of categories in dG of NSsites models

        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

   Small_Diff = .5e-6
    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.

在此目錄下開啟命令列

輸入一下命令即可

codeml

 

 當前目錄下就會出現結果檔案 test.txt  以及其他檔案了

 

在過程中我遇到過許多報錯提供給大家參考一下

67 columns are converted into ??? because of stop codons

這個報錯是因為沒有去除檔案中的終止密碼子，可以參考上面的步驟去除

 

Error: Error in sequence data file: . in 1st seq.?.

Error: check #seqs and tree: perhaps too many '('?.

Make sure to separate the sequence from its name by 2 or more spaces.

以上報錯均為你的序列檔案內容/格式有問題，麻煩按照上面的步驟重新生成序列檔案或者參考其他人的檔案格式

 

相關文章