But after reading this tweet, you may know part of it.

TBtools has been open to the outside world for more than two years, and from time to time, familiar and unfamiliar people will talk to me about TBtools. TBtools may be different in everyone's cognition.

Some people think that TBtools just delay their so-called bioinformatics research.

Some people say that TBtools guarantees their graduation.

It is also said that TBtools sent him an article.

Or, TBtools. .

I started writing TBtools three years ago. The function is very simple, mainly doing sequence extraction and also doing BlastWrapper (not robust at that time). The purpose is pure. The people in the research group will not ask me to extract the sequence, but they can also directly fry it to the transcription group to find the sequence. At that time, friends who contacted TBtools probably thought so.

Of course, I later made various enhancements to this aspect, which also ensured its current robustness. An input window which supports different inputs, whether extracting the full length of a sequence or extracting a sequence fragment; Not only supports ID extraction, but also supports ID substring matching. ...

In addition, the function of sequence extraction based on gff3 is added, such as extracting full-length CDS and full-length exons of all sequences, and even extracting all promoter sequences of a species in batches at one time.

In addition to Blast Wrapper, you may need to call external programs, so it's muscle (mainly because the NW algorithm I implemented is inefficient, so I won't mention it when it is used for multi-sequence alignment).

You can see it in the submenu.

Relatively rich in functions, including

Whether directly comparing two sequences, two sequence files or two designated intervals of two genomes, GUI has been provided in Blast and TBtools. And the four visualization methods can often meet the needs of most people.

take for example

Later, because Blast2GO was too slow. Based on the logic of IDmapping, I basically wrote a function of GO annotation. Of course, it may be more important to directly write the functions of GO and KEGG concentration analysis. So later, many friends of non-model creatures thought that TBtools actually did this. It also includes some visualizations, such as the secondary visualization of Go. Later, I also wrote some visualizations of the condensed results.

Slowly, I found that web-based tools, such as Venny, are obviously very small Wayne drawing function, and the network is too poor. Waiting for the buffer always takes up too much of my time. It should be localized. So I simply wrote a venn diagram tool that supports up to six groups. Of course, there are also late unpopular plot tools.

Genes displayed on chromosomes, tools such as MapChart.

In addition, due to some tools, such as heat map drawing, I think it is really inconvenient to use. Or there are too few parameters, or various details are not easy to adjust. So I also wrote a heat map tool.

Therefore, some friends may really think that your tool is just a drawing toolkit.

Venn diagram and disturbing diagram

Of course, you can also draw SeqLogo directly.

Based on my previous tweets, generally speaking, with TBtools, you can complete common gene family analysis without any command line or Linux or virtual machine operation.

Generally include tools are:

It seems that some training institutions provide online and offline gene family analysis training, and all kinds of virtual machines, Linux, commands and scripts that need to be used can be thrown away. Common gene family analysis projects may only need TBtools.

To this end, friends began to define TBtools: TBtools is a gene family analysis toolkit. In my opinion, in fact, these friends have a great misunderstanding about TBtools. I never thought of writing a tool for gene family analysis. Not because TBtools is a tool for gene family analysis, but because gene family analysis itself is the basic skill of biological data analysis that everyone needs and understands. I just simplified the realization of these skills.

As follows, in the TBtools I wrote, many people may not think of functions.

TBtools is not so much a tool for gene family analysis as a tool for comparative genome analysis, so it looks taller.

In the past half month, under the arrangement of the research group, I participated in some work related to genome analysis;

Genome analysis itself is actually an intellectual and physical activity. In the process of analysis, we also found some analytical methods that may allow people to obtain biological information from them.

So I spent two nights writing several tools.

In addition, some tools existing in TBtools before are believed to be helpful to friends who do genome analysis.

But please note that I can't guarantee the use of these tools unless I sponsor the outdoor development activities or cooperative units of our research group.

MCScanX is a common tool for comparative genome analysis. I have packaged it into TBtools, so even windows users can easily analyze it. In addition, users do not need to ensure that the gff file and the blast file have the same name.

For more information about this tool, please see the tweet before the official account of WeChat.

The calculation of Ka/Ks is often questioned. In fact, it is very easy to realize if the NG algorithm is simply calculated. At present, KaksCalculator2 and PAML are widely used. These two softwares are both Daniel software. In TBtools, I finally opened the NG computing logic realized last year or the year before, and played a very convenient GUI. Users can calculate information directly with almost only CDS sequences and gene pairs, without wasting time on file format arrangement.

Tools are constantly being optimized and developed.

The threshold of analysis will also be constantly broken.

Perhaps making everyone capable of some analysis is also a way to promote the development of some things.

Welcome friends who have not joined the TBtools QQ group. Join!

Every summer, the research group has internal training for students' information, mainly for freshmen in the laboratory (and members who are mainly engaged in wet experiments). I have always received the idea that other research groups want to know the data analysis of students' letters from our research group. Therefore, after the proposal of the doctoral supervisor and the discussion of the research group, we plan to increase 10 students' basic training places this summer (previously only in the research group, not open to the public). See/