说明文档：MEGAX-Help
- MEGA | 多序列比对及系统发育树的构建
ClustalW和MUSCLE - 如何使用MEGA软件构建系统发育树_速成实用经验
可用来建树的数据： DNA or Protein （染色体基因、线粒体、叶绿体、16S、基因保守区（MLST、domain序列）等）；可用来建树的方法：NJ（邻接法）、ML（最大似然法）、MP（最大简约法）、Bayes (贝叶斯法)；可用来建树的模型：DNA（GTR、TN93、HKY等）、Protein（JTT、WAG、LG等）。
E value
在BLAST结果页概述栏中，E value是默认按照由低到高的顺序排列。E value代表的是被比对的序列不相关的可能性，因此E value越小，代表序列相关性越大。若是E value无限趋近于0，则表示我们要检测的序列是完全匹配的。
Total Score
在概述栏中，Total Score分值越高，说明被BLAST的序列特异性越好。Total Score也是按照分值从高到低排列的。
Per.Ident
在概述栏中，Per.Ident代表了所在行的序列与被BLAST的序列的相似度。Per.Ident越大，表示该序列与被测序列相似度高，一般Per.Ident>97%就可以认为该序列与被测序列属于同属。
模式菌株：模式菌株（type strains）又称标准菌株，通常需要由至少两个不同国家的专门保藏机构保藏的菌株，一个菌株在同一个保藏机构有且仅有永久保藏号。保藏菌株是否是标准菌株的标志是在菌株名后有一个上标的T (Type)，每种菌可以有多个标准菌株。
外源菌：类似于“外群”，为了让查询菌的序列与相似序列更好地聚合，使得构建的系统发育树更具有可信度而引入的菌种。外源菌的获取：可以先查询目标序列的所属属，再查其所属科级下的其他属。最后，去NCBI官网直接搜索该属名，选择一个对应的扩增区的模式菌株的序列即可尝试用于建树。
Original tree 与Bootstrap consensus tree有什么区别？
1）在构建系统树时，使用了Bootstrap法进行检验。在做Bootstrap时，以原序列为蓝本随机重组生成新的序列，重复估算模型。如果原序列计算得到的分枝在新Bootstrap中依然频繁出现，则该分枝的可信度高。分枝在Bootstrap中出现的频率就是表征分枝可信度的参数；
2）Original Tree是步长检验构建的 N次株树中的最优系统树。未经过多棵树合并，所以Original Tree上有计算得到的距离数据，可以精确地表征两个基因的亲缘远近；MEGA形成的Original Tree上也有频率参数，实际来自Bootstrap Consensus Tree的对应分枝；
3）Bootstrap Consensus Tree 是很多次Bootstrap得到的平均结果，它不包含进化距离信息（在设置View时无法调用，也没有意义），分枝上的数字代表该分枝的频率参数，即经步长检验有百分之几的树具有这根树枝，反应了该树枝的可信度。另外，它的拓扑结构也可能与Original Tree很不相同。
(base) xxx@xxx-ThinkCentre-E97:~/Downloads$ /usr/bin/mega --debug
/usr/lib/mega/mega: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/mega/mega)
一般说来，MEGA适用于对少量的序列进行比对和画Tree，如需处理大量或海量的序列数据，建议使用ARB。？？？
解决办法1. 问题：libc.so.6: version ‘GLIBC_2.34‘ not found 高效解决办法这个办法谨慎使用
base) xxx@xxx-ThinkCentre-E97:~/Downloads$ strings /lib/x86_64-linux-gnu/libc.so.6 | grep GLIBC_
GLIBC_2.2.5
GLIBC_2.2.6
GLIBC_2.3
GLIBC_2.3.2
GLIBC_2.3.3
GLIBC_2.3.4
GLIBC_2.4
GLIBC_2.5
GLIBC_2.6
GLIBC_2.7
GLIBC_2.8
GLIBC_2.9
GLIBC_2.10
GLIBC_2.11
GLIBC_2.12
GLIBC_2.13
GLIBC_2.14
GLIBC_2.15
GLIBC_2.16
GLIBC_2.17
GLIBC_2.18
GLIBC_2.22
GLIBC_2.23
GLIBC_2.24
GLIBC_2.25
GLIBC_2.26
GLIBC_2.27
GLIBC_2.28
GLIBC_2.29
GLIBC_2.30
GLIBC_PRIVATE
到更新这一步不像别人的那么顺利，所以我没有按上面的办法。
(base) xxx@xxx-ThinkCentre-E97:~/Downloads$ sudo apt update
Get:2 http://mirrors.aliyun.com/ubuntu jammy InRelease [270 kB]
Hit:1 https://packages.microsoft.com/repos/code stable InRelease
Get:3 https://dl.google.com/linux/chrome/deb stable InRelease [1,825 B]
Err:3 https://dl.google.com/linux/chrome/deb stable InRelease
The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E88979FB9B30ACF2
Hit:4 https://linux.teamviewer.com/deb stable InRelease
Get:5 http://mirrors.aliyun.com/ubuntu jammy/main i386 Packages [1,040 kB]
Hit:6 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal InRelease
Get:7 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates InRelease [128 kB]
Get:8 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/universe amd64 Packages [1,217 kB]
Get:9 http://mirrors.aliyun.com/ubuntu jammy/main amd64 Packages [1,395 kB]
Get:10 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/universe Translation-en [293 kB]
Get:11 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/universe amd64 c-n-f Metadata [27.8 kB]
Get:12 http://security.ubuntu.com/ubuntu focal-security InRelease [128 kB]
Ign:13 http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal InRelease
Get:14 http://security.ubuntu.com/ubuntu focal-security/universe amd64 c-n-f Metadata [21.0 kB]
Err:15 http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal Release
404 Not Found [IP: 185.125.190.80 80]
Get:16 http://mirrors.aliyun.com/ubuntu jammy/main Translation-en [510 kB]
Get:17 http://mirrors.aliyun.com/ubuntu jammy/main amd64 DEP-11 Metadata [423 kB]
Get:18 http://mirrors.aliyun.com/ubuntu jammy/main DEP-11 48x48 Icons [100.0 kB]
Get:19 http://mirrors.aliyun.com/ubuntu jammy/main DEP-11 64x64 Icons [148 kB]
Get:20 http://mirrors.aliyun.com/ubuntu jammy/main DEP-11 64x64@2 Icons [15.8 kB]
Get:21 http://mirrors.aliyun.com/ubuntu jammy/main amd64 c-n-f Metadata [30.3 kB]
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://dl.google.com/linux/chrome/deb stable InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E88979FB9B30ACF2
E: The repository 'http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
容器法
(base) xxx@xxx-ThinkCentre-E97:~$ sudo apt-get update
Hit:1 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal InRelease
Hit:3 https://packages.microsoft.com/repos/code stable InRelease
Hit:2 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates InRelease
Get:4 https://dl.google.com/linux/chrome/deb stable InRelease [1,825 B]
Ign:5 http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal InRelease
Err:4 https://dl.google.com/linux/chrome/deb stable InRelease
The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E88979FB9B30ACF2
Err:6 http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal Release
404 Not Found [IP: 185.125.190.80 80]
Hit:7 http://security.ubuntu.com/ubuntu focal-security InRelease
Hit:8 https://linux.teamviewer.com/deb stable InRelease
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://dl.google.com/linux/chrome/deb stable InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E88979FB9B30ACF2
E: The repository 'http://ppa.launchpad.net/ubuntu-wine/ppa/ubuntu focal Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
(base) yhm@yhm-ThinkCentre-E97:~$ sudo apt-get install docker.io
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
bridge-utils containerd pigz runc ubuntu-fan
Suggested packages:
ifupdown aufs-tools btrfs-progs cgroupfs-mount | cgroup-lite debootstrap docker-doc rinse zfs-fuse | zfsutils
The following NEW packages will be installed:
bridge-utils containerd docker.io pigz runc ubuntu-fan
0 upgraded, 6 newly installed, 0 to remove and 130 not upgraded.
Need to get 68.6 MB of archives.
After this operation, 283 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal/universe amd64 pigz amd64 2.4-1 [57.4 kB]
Get:2 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal/main amd64 bridge-utils amd64 1.6-2ubuntu1 [30.5 kB]
Get:3 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/main amd64 runc amd64 1.1.12-0ubuntu2~20.04.1 [8,066 kB]
Get:4 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/main amd64 containerd amd64 1.7.12-0ubuntu2~20.04.1 [34.1 MB]
Get:5 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/universe amd64 docker.io amd64 24.0.7-0ubuntu2~20.04.1 [26.3 MB]
Get:6 http://mirrors.tuna.tsinghua.edu.cn/ubuntu focal-updates/main amd64 ubuntu-fan all 0.12.13ubuntu0.1 [34.4 kB]
Fetched 68.6 MB in 20s (3,505 kB/s)
Preconfiguring packages ...
Selecting previously unselected package pigz.
(Reading database ... 257723 files and directories currently installed.)
Preparing to unpack .../0-pigz_2.4-1_amd64.deb ...
Unpacking pigz (2.4-1) ...
Selecting previously unselected package bridge-utils.
Preparing to unpack .../1-bridge-utils_1.6-2ubuntu1_amd64.deb ...
Unpacking bridge-utils (1.6-2ubuntu1) ...
Selecting previously unselected package runc.
Preparing to unpack .../2-runc_1.1.12-0ubuntu2~20.04.1_amd64.deb ...
Unpacking runc (1.1.12-0ubuntu2~20.04.1) ...
Selecting previously unselected package containerd.
Preparing to unpack .../3-containerd_1.7.12-0ubuntu2~20.04.1_amd64.deb ...
Unpacking containerd (1.7.12-0ubuntu2~20.04.1) ...
Selecting previously unselected package docker.io.
Preparing to unpack .../4-docker.io_24.0.7-0ubuntu2~20.04.1_amd64.deb ...
Unpacking docker.io (24.0.7-0ubuntu2~20.04.1) ...
Selecting previously unselected package ubuntu-fan.
Preparing to unpack .../5-ubuntu-fan_0.12.13ubuntu0.1_all.deb ...
Unpacking ubuntu-fan (0.12.13ubuntu0.1) ...
Setting up runc (1.1.12-0ubuntu2~20.04.1) ...
Setting up bridge-utils (1.6-2ubuntu1) ...
Setting up pigz (2.4-1) ...
Setting up containerd (1.7.12-0ubuntu2~20.04.1) ...
Created symlink /etc/systemd/system/multi-user.target.wants/containerd.service → /lib/systemd/system/containerd.service.
Setting up ubuntu-fan (0.12.13ubuntu0.1) ...
Created symlink /etc/systemd/system/multi-user.target.wants/ubuntu-fan.service → /lib/systemd/system/ubuntu-fan.service.
Setting up docker.io (24.0.7-0ubuntu2~20.04.1) ...
Adding group `docker' (GID 136) ...
Done.
Created symlink /etc/systemd/system/multi-user.target.wants/docker.service → /lib/systemd/system/docker.service.
Created symlink /etc/systemd/system/sockets.target.wants/docker.socket → /lib/systemd/system/docker.socket.
Processing triggers for systemd (245.4-4ubuntu3.20) ...
Processing triggers for man-db (2.9.1-1) ...
(base) xxx@xxx-ThinkCentre-E97:~$ sudo systemctl start docker
(base) xxx@xxx-ThinkCentre-E97:~$ sudo systemctl enable docker
(base) xxx@xxx-ThinkCentre-E97:~$ sudo dpkg -r mega
[sudo] password for xxx:
(Reading database ... 258054 files and directories currently installed.)
Removing mega (11.0.13) ...
dpkg: warning: while removing mega, directory '/usr/local/share/man/man1' not empty so not removed
Processing triggers for gnome-menus (3.36.0-1ubuntu1) ...
Processing triggers for desktop-file-utils (0.24-1ubuntu3) ...
Processing triggers for mime-support (3.64ubuntu1) ...
Processing triggers for man-db (2.9.1-1) ...
(想着在Ubuntu上装MEGA太麻烦了，先搁置在这儿了)
4. Linux环境下解决依赖问题：libc.so.6(GLIBC_2.14)(64bit) is needed by
在Linux操作系统中，动态链接库（Dynamic Linking Library）是应用程序与操作系统之间的桥梁，它们允许程序在运行时链接和使用系统提供的各种功能。libc.so.6是glibc（GNU C Library）的核心动态链接库，它提供了许多基本的系统调用和函数。当某个程序或库需要特定版本的glibc时，如果系统上的glibc版本过低，就会出现依赖问题。
- /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34’ not found问题解决不推荐在直接升级运行环境libc版本，可能导致一些软件不兼容
- Ubuntu系统管理 ——使用dpkg安装、查看、卸载软件包
#dpkg 安装软件包
sudo dpkg -i xxx.deb
#dpkg 查看已安装软件包
dpkg -l
#dpkg 删除已安装软件包
sudo dpkg -r xxx
#dpkg 查看软件包的安装位置
dpkg -L xxx
- 生物信息之多序列比对，进化树分析，保守位点分析不知道这个网站是不是真的可以进行保守位点的分析MEME : http://meme-suite.org/tools/meme
2019
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