Training-materials

Repository of files used as materials for teaching and training

1. Useful sequence database and tools

a. NCBI https://www.ncbi.nlm.nih.gov/

b. Ensembl https://asia.ensembl.org/

c. UCSC Genome Browser

d. NCBI Genome Data Viewer

2. Analytical tools

a. MAFFT https://mafft.cbrc.jp/alignment/server/index.html

b. gVolante https://gvolante.riken.jp/

c. aLeaves https://treethinkers.nig.ac.jp/aleaves/

d. EBI EMBOSS Sequence Translation

e. JBrowse2 - the next-generation genome browser

f. D-Genies - for dot plot large genomes in an interactive, efficient and simple way

3. Other web sites

a. Genome sequence data availability for species in the Japanese Red List

b. Encyclopedia of Life

c. iNaturalist

d. Timetree of life

e. OneZoom Tree of Life Explorer

f. Tree viewer on T-Rex

4. Miscellaneous

a. Sequence search example at NCBI

b. Mouse FoxG1 entry at NCBI

c. Example tree for FoxG1 genes and their relatives (Hara et al., 2018)

d. Whale shark rhodopsin evolution ( English | Japanese )

e. Animal Genome Size Database

f. Plant DNA C-value database