Tools for phylogenetic footprinting purposes
  
                   
     
Transcription factor binding site detection using phylogenetic footprinting
     
                   
                   
 

Genomic alignment / exon detection /gene finding

   General genomic sequence analysis tools   Genomic databases  

Transcription factor site prediction

    
  Pipmaker Aligns two DNA sequences, returns alignment and percent identity plot PromotorInspector Predicts promotor localization on a genomic sequence Ensembl (human) Annotated public human sequencing effort ConSite Transcription factor binding site detection using phylogenetic footprinting  
  Orthoseq Alignment and exon prediction in orthologous nucleotide sequences RepeatMasker screens DNA sequences against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions. Ensembl (mouse) Annotated public mouse sequencing effort      
  ClustalW Standard tool for multiple sequence alignment CpG CpG islands prediction Gene portals   Pattern finding    
  Glass Alignment of orthologous genomic sequences    

Genelynx

 Portal to the human genome Meme/Mast Motif Discovery and Search  
  SGP1 Exon prediction based on sequence comparison     Flybase Comprehensive gene portal for Drosophila Gibbs Motif Sampler Motif identification in DNA or protein sequences  
  GenScan Ab initio prediction of locations of exon-intro structures in genomic sequence     Wormbase Comprehensive gene portal for C.elegans and closely related nematodes Anspec    
  Grail Gene recognitin and assembly     Tair Comprehensive gene portal for A. thaliana Splice signal detection    
  GeneID Ab initio prediction of locations of exon-intro structures in genomic sequence         Netgene2 Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA  
  Rosetta Human exon prediction based on orthologous sequence comparison              
  Twinscan Human exon prediction based on orthologous sequence comparison              
  Dotter Graphical dotplot program for detailed comparison of two sequences              
  HMMgene 1.1 Prediction of vertebrate and C. elegans genes