java 调用mafft 和 mothur

        Runtime.getRuntime().exec("C:/Windows/System32/cmd.exe /c start  D:\untitled\mafft.bat --auto --localpair --out LS1A_final_uniqueseq_align.fasta LS1A_final_uniqueseq_add_ref.fasta");

    Runtime.getRuntime().exec("C:/Windows/System32/cmd.exe /c start D:\liyang\command_s\mothur.exe " +
            ""#screen.seqs(fasta= LS1A_final_uniqueseq_out.fa,minlength=400,maxlength=430)""); // 通过cmd窗口执行命令