Quick links to some typical sequence-based analysis/prediction tools

Splicing Prediction/Annotation
NetGene2 http://www.cbs.dtu.dk/services/NetGene2/
GENSCAN http://genes.mit.edu/GENSCAN/
NNSplice http://www.fruitfly.org/seq_tools/splice/
SpliceView http://bioinfo.itb.cnr.it/oriel/splice-view/
GeneSplicer http://www.cs.jhu.edu/~genomics/GeneSplicer/gene_spl/
MaxEntScan http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq/
SplicePort http://spliceport.cbcb.umd.edu/
SD-Score https://www.med.nagoya-u.ac.jp/neurogenetics/SD_Score/sd_score/
Human Splicing Finder http://www.umd.be/HSF3/HSF/
CRYP-SKIP http://cryp-skip.img.cas.cz/
Spliceman http://fairbrother.biomed.brown.edu/spliceman/
RegRNA http://regrna2.mbc.nctu.edu.tw/index.html/

Sequnce Alignment to Reference Genome/Protein Sequences
BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi/
BLAT http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgBlat/

Mutiple Sequnce Alignment
MUSCLE https://www.ebi.ac.uk/Tools/msa/muscle/
MAFFT https://www.ebi.ac.uk/Tools/msa/mafft/
Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/
T-Coffee https://www.ebi.ac.uk/Tools/msa/tcoffee/

Phylogenetic Analyses
MEGA https://www.megasoftware.net/
IQ-TREE http://www.iqtree.org/
PAML http://abacus.gene.ucl.ac.uk/software/paml.html/

Protein Structure Prediction
ScanProsite https://prosite.expasy.org/scanprosite/
SWISS-MODEL https://swissmodel.expasy.org/
SPIDER http://sparks-lab.org/server/SPIDER3/

Miscellaneous Protein Sequence-based Tools
InterPro http://www.ebi.ac.uk/interpro/
HMMER https://www.ebi.ac.uk/Tools/hmmer/
POSSUM http://possum.erc.monash.edu/index.jsp/
PROFEAT http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi/

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