1) Choose a database:

Genbank / EMBL-Bank

DPDB (sequences of the Drosophila genus)

MamPol (sequences of the Mammalia class)

 

2) Enter a list of:

ORGANISMS and/or GENES:

ORGANISMS, TAXONOMY GROUPS OR ALIASES:		(e.g. Drosophila melanogaster, Cetacea or cow) (a new line for each item)
GENES:		(e.g. Actn) (a new line for each gene)

ACCESSION NUMBERS:

(e.g. AY219224 if database is Genbank, or DPseq000526 if database is DPDB, or MAMseq000526 if database is MamPol) (a new line for each accession number)

 

Enter a list of SEQUENCES:

Upload a file:

FORMATS SUPPORTED: - Unaligned sequences: FASTA (use the format >Organism|Gene in each sequence header if you want to specify this information) or GENBANK (each record ends with // in a new line) - Aligned sequences: FASTA (use the format >Organism|Gene in each sequence header if you want to specify this information)

 

	ONLY IF SEQUENCES FORMAT IS FASTA
	Codon start:  Assign all sequences to: 1 2 3, or change the values below*:		I want PDA to:
			Align my sequences Do not align my sequences (only if input sequences are already aligned)
	* If you uploaded a file with the sequences, please write a line foreach sequence with its codon start as follows:    Sequence 1 --> Codon start = 1    Sequence 2 --> Codon start = 1    etc.

 

1) Optional analyses:

Synonymous and Non-Synonymous Substitutions (in coding regions only)

Linkage Disequilibrium (in exons and introns only)
             Sliding Window Length (100 max):

Codon Bias (in coding regions only)
 

2) Regions to be studied separately (CDS, exon and intron will be selected automatically with the optional analyses):	3) Alignments quality:
- - - - - - - - - SELECT - - - - - - - - - attenuator C_region CAAT_signal CDS conflict D-loop D_segment enhancer exon GC_signal gene iDNA intron J_segment LTR mat_peptide misc_binding misc_difference misc_feature misc_recomb misc_RNA misc_signal misc_structure modified_base mRNA N_region old_sequence polyA_signal precursor_RNA prim_transcript primer_bind promoter protein_bind RBS repeat_region repeat_unit rep_origin rRNA S_region satellite scRNA sig_peptide snRNA snoRNA stem_loop STS TATA_signal terminator transit_peptide tRNA unsure V_region V_segment variation 3'clip 3'UTR 5'clip 5'UTR -10_signal -35_signal (use Ctrl or Ctrl+Alt to select more than one item)	Minimum number of sequences per category:
	Minimum Identity Score for pairwise comparisons (reduce or delete this parameter for very divergent sequences - HELP):	%
	Minimum sequences length:

4) Other parameters:

Use the Algorithm of Maximization of the Number of Informative Sites in the aligned sequences (AMNIS)     [Help]

 You can enter a TITLE for this analysis:   

Select an alignment program:
 

Muscle

ClustalW

T-Coffee

 

If ClustalW, you can change default parameters:

1) Fast Pairwise Alignment:

KTUP (WORD SIZE):	def: 12345
WINDOW LENGTH:	109876 def: 54321 0
SCORE TYPE:	def: percentabsolute
TOPDIAG:	10987 6def: 54321
PAIRGAP:	12 def: 34 5102550100250500

2) Multiple Alignment:

GAP OPEN	100 50def: 2510 521
END GAPS	offdef: on
GAP EXTENSION	0.050.5def: 1.02.5 5.07.510.0
GAP DISTANCES	109876 5def: 4321