If unsure which option to use, try 'mafft --auto input > output'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. The default gap scoring scheme has been changed in version 7.110 (2013 Oct). It tends to insert more gaps into gap-rich regions than previous versions. To disable this change, add the --leavegappyregion option.

如果不确定使用哪个选项，请尝试使用“mafft --auto input > output”。更多信息，请参见“mafft --help”，“mafft --man”以及mafft页面。在版本7.110（2013年10月）中， 默认的间隙评分方案已更改。它倾向于在间隙丰富的区域插入更多的间隙比以前的版本。如果要禁用此更改，请添加--leavegappyregion选项。

相关问题

High speed: % mafft in > out % mafft --retree 1 in > out (fast) High accuracy (for <~200 sequences x <~2,000 aa/nt): % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) If unsure which option to use: % mafft --auto in > out --op # : Gap opening penalty, default: 1.53 --ep # : Offset (works like gap extension penalty), default: 0.0 --maxiterate # : Maximum number of iterative refinement, default: 0 --clustalout : Output: clustal format, default: fasta --reorder : Outorder: aligned, default: input order --quiet : Do not report progress --thread # : Number of threads (if unsure, --thread -1)

这是mafft的一些常用命令和选项，用于在不同情况下生成高速或高精度的序列比对结果。以下是各个选项的含义：

1. High speed: 这是用于生成快速比对结果的选项。使用“mafft in > out”或“mafft --retree 1 in > out”命令可以获得快速比对结果。

2. High accuracy: 这是用于生成高精度比对结果的选项。使用“mafft --maxiterate 1000 --localpair in > out”、“mafft --maxiterate 1000 --genafpair in > out”或“mafft --maxiterate 1000 --globalpair in > out”命令可以获得高精度比对结果。

3. If unsure which option to use: 如果不确定应该使用哪个选项，则可以使用“mafft --auto in > out”命令。mafft将根据序列的数量和长度自动选择适当的比对选项。

4. --op #: Gap opening penalty。这是一个用于指定序列中插入空位（gap）的惩罚系数，默认值为1.53。

5. --ep #: Offset。这个选项类似于gap extension penalty，用于指定插入空位时的额外惩罚， 默认值为0.0。

6. --maxiterate #: Maximum number of iterative refinement。这是指定迭代次数的选项，用于控制算法的收敛速度，默认值为0，表示不进行迭代。

7. --clustalout: 输出clustal格式比对结果，默认输出FASTA格式。

8. --reorder: 指定输出结果的序列顺序，可以选择“aligned”或“input order”。

9. --quiet: 不显示比对进度信息。

10. --thread #: 指定线程数，如果不确定，请使用“--thread -1”选项，mafft将自动选择最佳线程数。

这些选项的具体用法和参数取值可以在mafft的官方文档中找到。

cannot remount /dev/mapper/ubuntu--vg-ubuntu--lv read-write, is write-protected.

As an AI language model, I do not have the complete context of the situation. However, I can suggest some general solutions you can try:

1. Check if the file system is already mounted as read-only. You can use the "mount" command to check this. If it is mounted as read-only, try to remount it as read-write using the "mount -o remount,rw" command.

2. Check if the device is write-protected. If it is, you need to disable the write protection.

3. Check if there are any errors in the file system. You can use the "fsck" command to check and repair any errors.

4. Check if there are any issues with the storage device. It could be a hardware issue. You can try to connect the device to another machine to see if it works.

5. If none of the above solutions work, you may need to backup your data and reinstall the operating system.

Again, I would recommend seeking the help of a qualified technician if you are unsure of what to do.