Talk:Phylogenetic inference using transcriptomic data
1. Provide a brief introduction and internal or external links to transcriptomes and phylogeny separately. -Briefly explain that transcriptome data is one of the most important sources use for phylogeny/phylogenomics among many other methods such as genomic data, gene family based data, captured nucleotide data, expressed sequenced tags etc. So, if we use transcriptomes for phylogeny, explain what factors that we should take into account: e.g. tissue type, developmental stage, environmental conditions, depth of coverage are some ideas.
2. The last section, inferring phylogenetic relationships, is the most important section of this article. But, it needs more information. It is required to provide information regarding how transcriptomes are used in the major areas of phylogenomics (comparative transcriptomics is applied in gene expression-functional genomics, character evolution, key innovations, RNA-Seq phylogenetics) with examples (lots of research articles and external sources are available)
3. Public databases: There are some more sources worth to mention e.g. 1 kp project for plant transcriptomes, 1 kite-1000 insect transcriptome project etc.
4. In the current article, Orthology connects the link: Homology. But, that does not include information you want to provide here about the distinction between orthology and paralogy.
5. Mention more about methods of predicting orthology: start with BLAST and add clustering or building step, More information on pHMM, HAMSter etc.
6. A large number of algorithms used for orthology detection and assembly. This article mentioned some programs under the section: computationally inferring orthologs. However, I hope it is better to briefly introduce about the algorithms first and mention those programs apply them.
7. Assembly includes lots of terminology (e.g. singled end, paired end, mate pair, k-mer, scaffold) which are useful to mention with links to definitions. Hope you could also provide links to the following terms that you have already mentioned: E-value, percent alignment.
8. Use some diagrams to explain assembly methods/ bioinformatics work flow. Lots of bioinformatics steps/tools involve in transcriptome analysis. The main steps include obtaining raw data, assembly, annotation, orthology detection, compilation of multiple taxa, alignment, phylogenetic inference. A diagram including main steps and needed software/tool would be beneficial for the readers.
Overall, this is an important topic needed to be addressed in Wikipedia, main sections included in the article are satisfactory, and writing is great! I think the above aspects will also be useful to you.