Latex

Pseudocode

\documentclass{article}
\usepackage[margin=2.2in]{geometry}
\usepackage{algorithm}
\usepackage{algorithmic}

\begin{document}
\thispagestyle{empty}

\begin{algorithm}
\caption{Find internal deletions from multiply mapping reads}
\begin{algorithmic} 

\REQUIRE alignment sorted by readname
\FOR{$read$ in alignment}
  \STATE $segments \leftarrow$ all mappings of $read$
  \IF{$segments > 1$}
    \STATE $macs \leftarrow Powerset(segments)$
    \FOR{$m$ in $macs$}
      \STATE $overlap \leftarrow CheckOverlap(m)$
      \STATE $distance \leftarrow CheckDistance(m)$
      \STATE $quality \leftarrow CheckQuality(m)$
      \IF{$overlap \geq limit$}
        \STATE $Discard(m)$
        \ELSIF{$distance \geq limit$}
        \STATE $Discard(m)$
        \ELSIF{$quality < limit$}
        \STATE $Discard(m)$
      \ENDIF
      \STATE $scores \leftarrow CumulativeQuality(m)$
    \ENDFOR
    \STATE $HighScoringMac \leftarrow max(scores)$
    \STATE $NewCigarSting \leftarrow BuildCigar(HighScoringMac)$
  \ENDIF
\ENDFOR

\end{algorithmic}
\end{algorithm}
\end{document}

Compiling just figures, tables and pseudocode

latex algo.tex
dvips -E -D 300 algo.dvi
epstopdf algo.ps
# -E just compiles the figure or table; not an entire page

dvipng -T tight -D 300 file.dvi
# dvipng to create pngs; where -T tight is replacing -E

 

Many thanks go to Lukas Weilguny who created this code